diff options
Diffstat (limited to 'sci-biology')
167 files changed, 1569 insertions, 1216 deletions
diff --git a/sci-biology/OBO-Edit/ChangeLog b/sci-biology/OBO-Edit/ChangeLog new file mode 100644 index 000000000..e1de6ad37 --- /dev/null +++ b/sci-biology/OBO-Edit/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/OBO-Edit +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> OBO-Edit-2.1_beta8.ebuild: + Cleaned ebuild + diff --git a/sci-biology/OBO-Edit/Manifest b/sci-biology/OBO-Edit/Manifest index b12079377..7d3684c16 100644 --- a/sci-biology/OBO-Edit/Manifest +++ b/sci-biology/OBO-Edit/Manifest @@ -1,4 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + AUX response.varfile 161 RMD160 3fbf3bb5a79dafecefdd64314f4fcfbb05ecc8d0 SHA1 46c6214c7072221455e74a9aa502c85b8edca0be SHA256 4a5793bb5bf94fcb10732cf9f821eacfa41b8a36d1a5fc4bae76408f19d85c02 DIST oboedit_2_1_8_linux_install4j.rpm 51962024 RMD160 b1ce3c7704c2fbe5185e36c6ad6c63f7fcf065fb SHA1 6a8a1605b9d6f16b6dc34469442a520029135eaa SHA256 e29edfe6531be9f64235e2891426b3ecf9f5a12f0f0f09a0b461f440dbcacfdd -EBUILD OBO-Edit-2.1_beta8.ebuild 1202 RMD160 e344bfb70b7291a04f3a21e41d9a8cdbeb75af36 SHA1 7f3df8619ec1ca9d9fc0912e175a159d86ddd6da SHA256 41fcb00811757696c332c9d4d1941ea186d7265ab7d2bfe05c923e9486125b51 +EBUILD OBO-Edit-2.1_beta8.ebuild 1011 RMD160 9214f2ed58107aceb10259e9960380a2e42a508d SHA1 52ccbf82bb26a9764c73f43edd5749297c43bd0f SHA256 efbeebf397b2176e07fc80aaf020cd9d9e4d2b4523315a820939761d3902a8c7 +MISC ChangeLog 213 RMD160 b8548e6d5f3b28a81e670bea1bad94cf72b68541 SHA1 aed23b323ab6ec8f1ba26a4e0583e139d9b4c50e SHA256 60ac52b6c2696252417f779b77704412a18162fa69c7923c53722072ac6deb90 MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F9AUACgkQgAnW8HDreRaa7QCghXG6JSHPKGLWYGFRHT83RWD3 +oscAoJucwotuTlZpVfq0ImuGVTIQcThj +=RaKC +-----END PGP SIGNATURE----- diff --git a/sci-biology/OBO-Edit/OBO-Edit-2.1_beta8.ebuild b/sci-biology/OBO-Edit/OBO-Edit-2.1_beta8.ebuild index debd89f27..8842bcdb3 100644 --- a/sci-biology/OBO-Edit/OBO-Edit-2.1_beta8.ebuild +++ b/sci-biology/OBO-Edit/OBO-Edit-2.1_beta8.ebuild @@ -2,7 +2,9 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=4 + +inherit rpm DESCRIPTION="Java-based editor optimized for the OBO biological ontology file format" HOMEPAGE="http://www.oboedit.org/" @@ -15,19 +17,16 @@ KEYWORDS="~amd64 ~x86" IUSE="" DEPEND="app-arch/rpm2targz" -RDEPEND="${DEPEND} - virtual/jre" +RDEPEND="virtual/jre" -src_unpack() { - cd "${WORKDIR}" - rpm2targz "${DISTDIR}/oboedit_2_1_8_linux_install4j.rpm" || die - tar -xzf "${WORKDIR}/oboedit_2_1_8_linux_install4j.tar.gz" || die -} +S="${WORKDIR}"/opt src_install(){ # sh "${DISTDIR}"/oboedit_2_1_8_unix_install4j.sh -q -overwrite --var-file="${FILESDIR}"/response.varfile --destination="${D}"/opt/OBO-Edit2 - mkdir -p "${D}"/opt/ || die - cp -rp opt/OBO-Edit2 "${D}"/opt/ || die - find "${D}"/opt -name firstrun | xargs rm -f # drop a world writable file - find "${D}"/opt -name .svn | xargs rm -rf + find . -name firstrun -delete + find . -name .svn -exec rm -rf '{}' \; + + insinto /opt/ + doins -r OBO-Edit2 + chmod 755 "${ED}"/opt/OBO-Edit2/* } diff --git a/sci-biology/ONTO-PERL/ChangeLog b/sci-biology/ONTO-PERL/ChangeLog new file mode 100644 index 000000000..847ef31f3 --- /dev/null +++ b/sci-biology/ONTO-PERL/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/ONTO-PERL +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> ONTO-PERL-1.31.ebuild: + Cleaned ebuild, 'http://search.cpan.org/CPAN' found in thirdpartymirrors + diff --git a/sci-biology/ONTO-PERL/Manifest b/sci-biology/ONTO-PERL/Manifest index cea366935..66f2b8d5b 100644 --- a/sci-biology/ONTO-PERL/Manifest +++ b/sci-biology/ONTO-PERL/Manifest @@ -1,3 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + DIST ONTO-PERL-1.31.tar.gz 721117 RMD160 0253abe13b159578955aff5cd0b294ddc3c8c9ed SHA1 93147c710ab0c3e5d227c91ff22dea1de6d2c6fa SHA256 89a85cbe2f7ced1a394d863d9b6fbc54fae2cc8a3c2531fcaaebaf50489866b8 -EBUILD ONTO-PERL-1.31.ebuild 656 RMD160 e29e0b2bb9382c7cac680448c0e7a62850a2437f SHA1 f04ae934a75027f6f1f3f028994aab634bc0dc86 SHA256 3ab67cb3df24b53241929631c974c1b97455ad5977e4bc3ea587a2fa58bef316 +EBUILD ONTO-PERL-1.31.ebuild 549 RMD160 369b3febfed860468843bbf9ae3819c44929faf9 SHA1 84ef7853cae41bea9cc8c3ddf10eedd1429a5cf3 SHA256 cafd5f1e96a254aa4c8107214afe3795e6a6ced10a9dc6203b96e551f179dec3 +MISC ChangeLog 268 RMD160 7ee93ecde2424e9e58e287496593e5335ff877b0 SHA1 a5a25c4ccfee8d1f2c05c68ee0e869069bb31dff SHA256 2b597424fede3c8c80631c215da408b7050da0454e739b837d2a8563ddb6459e MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F8lEACgkQgAnW8HDreRboOACgxyF0eel2GS+hFJWZFkewTKAJ +l7EAoL/6f7pEw0MjEOHc4KkxAuGV160N +=3aoL +-----END PGP SIGNATURE----- diff --git a/sci-biology/ONTO-PERL/ONTO-PERL-1.31.ebuild b/sci-biology/ONTO-PERL/ONTO-PERL-1.31.ebuild index efb4f7a46..473a145f9 100644 --- a/sci-biology/ONTO-PERL/ONTO-PERL-1.31.ebuild +++ b/sci-biology/ONTO-PERL/ONTO-PERL-1.31.ebuild @@ -1,18 +1,19 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/dev-perl/Geo-IP/Geo-IP-1.38.ebuild,v 1.1 2009/05/19 12:22:20 tove Exp $ +# $Header: $ EAPI=2 MODULE_AUTHOR=EASR -inherit perl-module multilib + +inherit multilib perl-module DESCRIPTION="Manipulates OBO- and OWL-formatted ontologies (like the Gene Ontology)" +SRC_URI="mirror://cpan/authors/id/E/EA/EASR/ONTO-PERL/ONTO-PERL-1.31.tar.gz" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -SRC_URI="http://search.cpan.org/CPAN/authors/id/E/EA/EASR/ONTO-PERL/ONTO-PERL-1.31.tar.gz" DEPEND="" RDEPEND="${DEPEND} diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest index 0f80e3de9..b9e41a1a5 100644 --- a/sci-biology/amos/Manifest +++ b/sci-biology/amos/Manifest @@ -1,4 +1,13 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX amos.m4.patch 1597 RMD160 f59e198aa725132f9e63d95a7efb05281d83a26f SHA1 5f4dfd9ffc40b2d06a3e8b4996aed2cbbe1297e7 SHA256 c5015f3548b2465fe235a8f2906fc0da2ecc96e50ebe2d7818aa2e17202aa01d EBUILD amos-9999.ebuild 1443 RMD160 020608c038facb917a9b52fe33cf5a70964fcffb SHA1 092e11d2844a4ea917d91c8edfd3d0682408ad34 SHA256 8e6ed1e4926c6e13531dc719d751028d5499e093b58a38ba8fb542d0db00da61 -MISC ChangeLog 213 RMD160 de502e7771dc17bd94b9bcd73b8288ebeff8892c SHA1 c0ea21e961752ecc7d8ed29334a31beb631ffc00 SHA256 423e7fb2941c5d867e363f2c6cbd26ed39b5efee85724fd76ac3d3c1803bd2d5 -MISC metadata.xml 549 RMD160 aaaa14a78b782644b19b4319869cfe78d2db5836 SHA1 f587b263a39731a1af3c80854aa5959f8edb7db6 SHA256 175313bbe3f6d424690f879605a71e0e2661d84b4c4cdd884d4a5cb05c04c7b9 +MISC metadata.xml 557 RMD160 3c1fa25a5d69a810652841110b688036a6971a64 SHA1 004c2081cbbcc715c82273022e7f4afce45c6da6 SHA256 fd4ffdf2f6037866d7ff2acf02e8d0c6bc9950888c1276c3de09958d4b141509 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EwEoACgkQgAnW8HDreRZnVACdEvKREzWpDhIjVPoRWZUAm18J +ZwkAn0MRMmjUrZeECCipLdsKQmR7bYci +=hr7y +-----END PGP SIGNATURE----- diff --git a/sci-biology/apollo/Manifest b/sci-biology/apollo/Manifest index 056646de8..5f874bbc5 100644 --- a/sci-biology/apollo/Manifest +++ b/sci-biology/apollo/Manifest @@ -1,2 +1,12 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + EBUILD apollo-9999.ebuild 1048 RMD160 21152d198e3c6a17442d1cde53f4bdf81d6089a1 SHA1 637631379bc584f26caba8fd4f4faea0597ba13e SHA256 6c8177a03caa6e4166d055da0fcb9b88feb2edaf00e3d38f996f73f644c6dc47 -MISC metadata.xml 261 RMD160 ce19afc5fdd536a9eadb35a705f09613e3774e32 SHA1 b95b491e808c8dd5a106edae7e48af4f8d61f58a SHA256 e3766426d46af16432093cd9fb8a2df3862c77ef313ad175ca2ef60af5cee6f5 +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Ev5QACgkQgAnW8HDreRYwLgCeKqTedlqvgkrkXwKNBfFfYN9o +o40AoJ8xTGL9Ko6q8XwA0X222+RUCPr3 +=ALTA +-----END PGP SIGNATURE----- diff --git a/sci-biology/argo-bin/ChangeLog b/sci-biology/argo-bin/ChangeLog new file mode 100644 index 000000000..7f9152a7a --- /dev/null +++ b/sci-biology/argo-bin/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/argo-bin +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> argo-bin-1.0.31.ebuild: + Cleaned ebuild + diff --git a/sci-biology/argo-bin/Manifest b/sci-biology/argo-bin/Manifest index ddf9aded8..12adf4d3e 100644 --- a/sci-biology/argo-bin/Manifest +++ b/sci-biology/argo-bin/Manifest @@ -1,3 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + DIST argo.jar 26624770 RMD160 d789a09818e3d6d3cb87b11411c49959a050fa79 SHA1 305a668897ebd8f9c9c12484b3518a591121e51d SHA256 33ece2dba7ee5cc36f5aab99b3e7df2d641b261d86aacac00745e9d4a2e914cf -EBUILD argo-bin-1.0.31.ebuild 826 RMD160 43c29f959b336d944cd7864e5483f43fcd42a2dc SHA1 0b6778565dcc6d1f0a87340eefa2c9c5c5480586 SHA256 a4c2363eab488198df4762ecfc9f5a4549a0d58da895ddce6cbb4aaa0d7b6188 -MISC metadata.xml 261 RMD160 ce19afc5fdd536a9eadb35a705f09613e3774e32 SHA1 b95b491e808c8dd5a106edae7e48af4f8d61f58a SHA256 e3766426d46af16432093cd9fb8a2df3862c77ef313ad175ca2ef60af5cee6f5 +EBUILD argo-bin-1.0.31.ebuild 750 RMD160 48f92a7e0bc78e52758d23e03187a3c064b66ce4 SHA1 f0dd3eea6eeebd45c2e07f894d5d6f4ec031af61 SHA256 5a2c0b5e82bdac568e5d671730595a8969bdd7e33d051e3f2133379805302b90 +MISC ChangeLog 210 RMD160 c00a3a468c7cad5ff65f84c0d9f3357bc9fa25a9 SHA1 b98c0ed89efdef2754c6d89da9ae28b5bb93b544 SHA256 8789c4325700c8afd94e30292e96c792d1282177baa879b3ce548f08db288726 +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F75cACgkQgAnW8HDreRbZLgCeLx70kw5eOyWwmJv7iQTwcWxo +9DEAn0X1CgF0j1rrThydYJYRVfUwSX9+ +=ErKe +-----END PGP SIGNATURE----- diff --git a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild b/sci-biology/argo-bin/argo-bin-1.0.31.ebuild index ee72f80a9..7ed58fad2 100644 --- a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild +++ b/sci-biology/argo-bin/argo-bin-1.0.31.ebuild @@ -1,14 +1,12 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r2.ebuild,v 1.2 2010/10/10 21:20:04 ulm Exp $ -EAPI=3 +EAPI=4 -inherit toolchain-funcs java-utils-2 +inherit java-utils-2 toolchain-funcs -DESCRIPTION="The Argo Genome Browser is a production tool for - visualizing and manually annotating whole genomes - stored in .gff3 files" +DESCRIPTION="Visualization and manually annotating whole genomes" HOMEPAGE="http://www.broadinstitute.org/annotation/argo/" SRC_URI="http://www.broadinstitute.org/annotation/argo/argo.jar" #SRC_URI="http://www.broadinstitute.org/annotation/argo/src/workspace-2008-03-11.tgz" @@ -26,4 +24,3 @@ src_install() { java-pkg_newjar "${DISTDIR}"/argo.jar argo.jar java-pkg_dolauncher } - diff --git a/sci-biology/argo/Manifest b/sci-biology/argo/Manifest index a23395d9c..62322c09d 100644 --- a/sci-biology/argo/Manifest +++ b/sci-biology/argo/Manifest @@ -1,3 +1,13 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST workspace-2008-03-11.tgz 109194467 RMD160 873b9c3facfe872108a4c8849a774d5c8c74893f SHA1 382642ae8d7498bb8c21764fa625aa47b4107cfb SHA256 0ee6acb0ebdc17cfbedfedb8559ba950ddd4c5c4ef5f7875fa93f3fad885b99e -EBUILD argo-1.0.24.ebuild 935 RMD160 54eb968965979b8b37e236f94faa554ebb7d21df SHA1 65eda8fec914b3a43184e039c52a91d6381d8005 SHA256 f06f6d3ca2e10a5eee2e4f233bedfcacaaa918b4294d945a861399ffd95e40c3 -MISC metadata.xml 261 RMD160 ce19afc5fdd536a9eadb35a705f09613e3774e32 SHA1 b95b491e808c8dd5a106edae7e48af4f8d61f58a SHA256 e3766426d46af16432093cd9fb8a2df3862c77ef313ad175ca2ef60af5cee6f5 +EBUILD argo-1.0.24.ebuild 879 RMD160 7288ffba9db9f8380326957a0b2e780434b190fb SHA1 d662bcdf91e2a10bf6a49ae643d3d7552748f3ae SHA256 558fcb91ff7a7188d49a86343ae7c58ce5053995c0cdfd9e17fe7e7b8308e026 +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Ei+4ACgkQgAnW8HDreRav7wCdFTNQA2y8/m1P5MN+B1mIVE+l +5ucAnRUBfKPrUIvcaEfPasGiSs4CVkcM +=wbss +-----END PGP SIGNATURE----- diff --git a/sci-biology/argo/argo-1.0.24.ebuild b/sci-biology/argo/argo-1.0.24.ebuild index 30fba8746..055979850 100644 --- a/sci-biology/argo/argo-1.0.24.ebuild +++ b/sci-biology/argo/argo-1.0.24.ebuild @@ -4,11 +4,9 @@ EAPI=3 -inherit toolchain-funcs java-utils-2 java-pkg-2 java-ant-2 +inherit java-pkg-2 java-ant-2 java-utils-2 toolchain-funcs -DESCRIPTION="The Argo Genome Browser is a production tool for - visualizing and manually annotating whole genomes - stored in .gff3 files" +DESCRIPTION="Production tool for visualizing and manually annotating whole genomes" HOMEPAGE="http://www.broadinstitute.org/annotation/argo/" SRC_URI="http://www.broadinstitute.org/annotation/argo/src/workspace-2008-03-11.tgz" @@ -18,8 +16,9 @@ KEYWORDS="~amd64 ~x86" IUSE="" RDEPEND=">=virtual/jre-1.5" -DEPEND=">=virtual/jdk-1.5 - dev-java/ant-core" +DEPEND=" + >=virtual/jdk-1.5 + dev-java/ant-core" S="${WORKDIR}"/workspace-2008-03-11 diff --git a/sci-biology/autoeditor/ChangeLog b/sci-biology/autoeditor/ChangeLog new file mode 100644 index 000000000..a95258201 --- /dev/null +++ b/sci-biology/autoeditor/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/autoeditor +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> autoeditor-1.20.ebuild: + Shorten Summary + diff --git a/sci-biology/autoeditor/Manifest b/sci-biology/autoeditor/Manifest index c6f9f202c..641dc429b 100644 --- a/sci-biology/autoeditor/Manifest +++ b/sci-biology/autoeditor/Manifest @@ -1,6 +1,17 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX Makefile.patch 3051 RMD160 bca80507a7d1b401a96b654e7049a54c8f68bd05 SHA1 453ce786ab004f25eb19842d8558ad450bb34560 SHA256 534d67e7effdb072d6a2c7469e67b50ff82da5c5c9bf16de57d30609b024055d AUX sample_expected.out 1118 RMD160 38f3a997add481e6ac8b2f981e32aab6113302ce SHA1 5c1afa013888ccdeb4325935a4bc362dfdebe2e1 SHA256 bb51ba6b15a9916c65b0209742ff3dc3a8832c1355f65cbf35738ce88047ce9b DIST autoEditor-1.20-sample.tar.gz 71953287 RMD160 bfb859a3badec0db85ee31086d2574cd43ebe3a3 SHA1 a36668f1d041552229684c20d9789e7b6301d57e SHA256 f25beb3668ab2b3f2018e5e3b9615995ba5a16b5ce002ff50806287f28f5ef25 DIST autoEditor-1.20.tar.gz 2438903 RMD160 598ac977eb424959fc052b4c857ef4487b7e13f9 SHA1 985b5e880148a904b157295053945f9530718d30 SHA256 c0c399eda52a10deb0e0362b4caf909014768a4d08e90c900392cdf712cefd66 -EBUILD autoeditor-1.20.ebuild 1304 RMD160 1090965e8b9dcfdbf5ed192976dd2ddde4164cdb SHA1 17c7245826480ec3e3ea93b1f373a1077dbdec70 SHA256 a3f44b7e1eb317350ec8e676068601d164e50f997ff0d9919282d4d68abb5711 -MISC metadata.xml 1152 RMD160 0c202dd48bd4242879dccee9f566e9003857db84 SHA1 bf658a22a72370f46e76da50b1960f5fbb189aae SHA256 a6323415c0ec7864b776e4454845e6e659f23e978669c86aa4188ac0bbad24b8 +EBUILD autoeditor-1.20.ebuild 1134 RMD160 9a60610118475e6bdcfc54676887e1a809fa526f SHA1 297b5566c27274765b52345a6c943d62d750d00f SHA256 8e62b735c19f1ea2a5a1a9fc729fb55f68706f9d6ddf68c6e51eaad02a686345 +MISC ChangeLog 213 RMD160 dad86b527258c7be58b278fd8afcb94f83c4f9a1 SHA1 e37a2303e9c3d7f86446da6094bcb684ff1989bf SHA256 e3e26aff923684c1790497a3cb2c2b04a094d0dba50a2944de58008857873971 +MISC metadata.xml 1160 RMD160 1006598866055875c6ad7f39e0634def718002db SHA1 2b13d7786cc0dac0434b14bace3467126904ddc2 SHA256 fb86e548211f36d0f56372b98bd47ff6228e9e81862714937afb1292e9004079 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EwNcACgkQgAnW8HDreRb6RACgkYKEo++8/u1PQglFS2rPcO1y +Va4An3GZWl1Zj/OwpNTKqys8QJwLFVpn +=4wrn +-----END PGP SIGNATURE----- diff --git a/sci-biology/autoeditor/autoeditor-1.20.ebuild b/sci-biology/autoeditor/autoeditor-1.20.ebuild index bbe990805..f39f43dd5 100644 --- a/sci-biology/autoeditor/autoeditor-1.20.ebuild +++ b/sci-biology/autoeditor/autoeditor-1.20.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -6,20 +6,21 @@ EAPI=3 inherit eutils -DESCRIPTION="AutoEditor is a program that can automatically correct discrepancies in a -multiple alignment by reanalyzing the chromatograms of the discrepant bases." +DESCRIPTION="Automatic correct of discrepancies in multiple sequence alignments" HOMEPAGE="http://sourceforge.net/apps/mediawiki/amos/index.php?title=AutoEditor" -SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/autoEditor/autoEditor-1.20.tar.gz - test? ( ftp://ftp.cbcb.umd.edu/pub/software/autoEditor/autoEditor-1.20-sample.tar.gz )" +SRC_URI=" + ftp://ftp.cbcb.umd.edu/pub/software/autoEditor/autoEditor-1.20.tar.gz + test? ( ftp://ftp.cbcb.umd.edu/pub/software/autoEditor/autoEditor-1.20-sample.tar.gz )" LICENSE="Artistic" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND=">=sci-libs/io_lib-1.8.11 - sys-libs/zlib - sci-biology/tigr-foundation-libs" +DEPEND=" + >=sci-libs/io_lib-1.8.11 + sci-biology/tigr-foundation-libs + sys-libs/zlib" RDEPEND="${DEPEND}" S="${WORKDIR}"/autoEditor-1.20 @@ -29,14 +30,6 @@ src_prepare(){ rm -rf TigrFoundation-2.0 || die "Failed to drop TigrFoundation-2.0/" } -src_compile(){ - emake || die -} - -src_install(){ - emake install DESTDIR="${D}" || die -} - # TODO: # * QA Notice: Package has poor programming practices which may compile # * fine but exhibit random runtime failures. diff --git a/sci-biology/bamtools/ChangeLog b/sci-biology/bamtools/ChangeLog new file mode 100644 index 000000000..111c436cf --- /dev/null +++ b/sci-biology/bamtools/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/bamtools +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> bamtools-9999.ebuild: + Moved from 'git' to 'git-2' + diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest index 2d1817498..0fc975819 100644 --- a/sci-biology/bamtools/Manifest +++ b/sci-biology/bamtools/Manifest @@ -1,4 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST bamtools-20101215.tar.gz 142100 RMD160 615f64659faaf21d0d83a11e9d0748b5220888be SHA1 1c5d44928434e9e99187035630724205d10bc337 SHA256 3b90c8317207398d94bb7b7cf6470ee8ae8f3b306332c498d1696c80659dce07 EBUILD bamtools-20101215.ebuild 758 RMD160 d0dd72604cfde877a8ce64261a964c2a145a4b15 SHA1 7c0d41b89cf09f0c0a81f7d9ed7a5a3d44ea3837 SHA256 740ee79b8830e455363c5aafb47fe44675000ab119b915107de48f95b4345415 -EBUILD bamtools-9999.ebuild 885 RMD160 ecfefc0a74541f88fa2a331ad6799be05bef80ea SHA1 c1f10f3348ee88c90e278dd6b33c6bebd910303a SHA256 3424284b41b44b8087629335fcb894d89b6d58493410270a65f5f1b6251c7543 -MISC metadata.xml 547 RMD160 1b58f37f70cc5873715f4b77795428f1f393b7ee SHA1 a1900126a5dee33d7c9ed138923ea2f0db28fa9d SHA256 4573902d3d9a0bc60d9e253439e87462cba88e1cf6dd2ac7e1be35242f38b4d8 +EBUILD bamtools-9999.ebuild 887 RMD160 edac08fd4f626ddcd46e70e7e3a33629975526e6 SHA1 2b451d5e08c68ede6b0cea58e32c295e9449ddb1 SHA256 d9c89d10dbe417fc40c60d97ca12059ee562c9a9e0da1c2f453c61478a129d97 +MISC ChangeLog 221 RMD160 68ce47391131977af697c1358c535193098e7f8a SHA1 9f93a33b9fd78f6b33225cdc7bf523f602e9cc45 SHA256 965f3bb7dc9bba900ee96e9a82fc344d9b58743d39f27a9a1ccaf69fe9ec31ad +MISC metadata.xml 555 RMD160 4562689d2995eb95550c28a48c7d9516b81bb572 SHA1 02ce41839a3b77ac7122a736b2dc71acc9408dc6 SHA256 8a592c3fc8ff1340d59d088fb6b1e5e3184433d6a1546985e09fa14b79869b09 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4ExvcACgkQgAnW8HDreRb9AgCghOuvXFxkcw3fHAPV4PTuTwD/ +UoAAoIlUD9lYLJRJ1QYyHKYPPEGo4bQT +=3c+9 +-----END PGP SIGNATURE----- diff --git a/sci-biology/bamtools/bamtools-9999.ebuild b/sci-biology/bamtools/bamtools-9999.ebuild index 6448e0a00..e23dc3974 100644 --- a/sci-biology/bamtools/bamtools-9999.ebuild +++ b/sci-biology/bamtools/bamtools-9999.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=3 -inherit cmake-utils git +inherit cmake-utils git-2 DESCRIPTION="BamTools provides a fast, flexible C++ API for reading and writing BAM files." HOMEPAGE="http://sourceforge.net/projects/bamtools" diff --git a/sci-biology/bedtools/ChangeLog b/sci-biology/bedtools/ChangeLog new file mode 100644 index 000000000..3fd80712f --- /dev/null +++ b/sci-biology/bedtools/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/bedtools +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> bedtools-2.10.1.ebuild: + SOme ebuild cleaning + diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest index 7f721ba90..e3af7c57a 100644 --- a/sci-biology/bedtools/Manifest +++ b/sci-biology/bedtools/Manifest @@ -1,3 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST BEDTools.v2.10.1.tar.gz 904396 RMD160 db6b9f103bff28a04479d243b05de7c8cb38c208 SHA1 67ece0f2747b6886de8ab9642365fa071d0fe32c SHA256 b128ee474827aad2a3bd8808aeaeca484120fc202ac5f1f7b805c21d0be76458 -EBUILD bedtools-2.10.1.ebuild 656 RMD160 618b0fa2740c6da5a3ace6300ce93d5199fe8edc SHA1 61f2299b782ab680895de9f3698142afe038f29f SHA256 b78bf69a0aa265139238ce3689cfdded2b3fd6c35007cbca1201e453c781a07b -MISC metadata.xml 365 RMD160 97d6bbddf5c26e472d3c6c19ec50c2db87d88dda SHA1 8e10d068960e7e258db3e33397f679dc56bf0545 SHA256 0209b66105b6f3fd1059f6c16366807c71d96fe6021b80cd115adc745192981b +EBUILD bedtools-2.10.1.ebuild 485 RMD160 039c6cbbceb4154a022fe95635bb00fac8e443fc SHA1 bacae16709812d7687b14a9f07fe6a4f680f38fa SHA256 efb1a05b1f80ac6a04747572380b6fe53827423cfa7c0a4e63f0f1228d4238ad +MISC ChangeLog 216 RMD160 6779ba4504285979c47f966da1e0141322da629f SHA1 4fc8043870c49461873e220c9768396ea90376a3 SHA256 ebf9a0ba64734c49cad21cadb00c7c5633fc9680211dbf60975b5eb06a3a4907 +MISC metadata.xml 373 RMD160 492d63a640c8667cd2c3e48f9f79916348eaa425 SHA1 57afd5cc95b7a6fd4ed4ecdc8a2dd40f3036d6ba SHA256 9cd28401c75e322432ebbf23f9e9ba4c32154e951171de78c83668a33147e042 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Ex3AACgkQgAnW8HDreRbomwCgwPWuLzeea794YNTaqD2BSnlJ +lf0AoJ++a1yEa9u42KNdO7XvDohVFNbo +=sZl+ +-----END PGP SIGNATURE----- diff --git a/sci-biology/bedtools/bedtools-2.10.1.ebuild b/sci-biology/bedtools/bedtools-2.10.1.ebuild index f03a4f761..541b05647 100644 --- a/sci-biology/bedtools/bedtools-2.10.1.ebuild +++ b/sci-biology/bedtools/bedtools-2.10.1.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=4 -DESCRIPTION="BEDTools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats" +DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats" HOMEPAGE="http://code.google.com/p/bedtools/" SRC_URI="http://bedtools.googlecode.com/files/BEDTools.v${PV}.tar.gz" @@ -13,16 +13,8 @@ SLOT="0" KEYWORDS="~x86 ~amd64" IUSE="" -DEPEND="" -RDEPEND="${DEPEND}" - -src_compile(){ - cd BEDTools-Version-2.10.1 || die - emake all || die -} +S="${WORKDIR}"BEDTools-Version-${PV} src_install(){ - cd BEDTools-Version-2.10.1 || die - mv bin/overlap bin/bt_ovelap # prevent file collision with sci-biology/wgs-assembler - dobin bin/* + newbin bin/overlap bt_ovelap } diff --git a/sci-biology/caftools/Manifest b/sci-biology/caftools/Manifest index c832cecf0..82c2f4fcc 100644 --- a/sci-biology/caftools/Manifest +++ b/sci-biology/caftools/Manifest @@ -1,7 +1,17 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX Makefile.in-2.0.2.patch 1619 RMD160 a36fc2e878424df24e4a2501769b5959d2997362 SHA1 255d22883c245bbbcb29cf1afaeafc08d067bd8f SHA256 4d24755beabe400afcfcdb987bbe85d117a2098ce6f05879cc813166448569c2 AUX Makefile.in.patch 1633 RMD160 2942a5da7112bfb9f9c6bbd40d26b85d6688265b SHA1 b96e4ebd6b3805c04f7690b240729ca5228dfd3e SHA256 c8bb87d532e664683b41ae0f46a08f9232e1724a574f8a03e658130b0e13d223 DIST caftools-2.0.2.tar.gz 2645554 RMD160 66ebb894e8899e10349742de1bae67a565a35a9c SHA1 071a170d265ddef46ae2f5effa478421e9cce6ff SHA256 7be5eafbd6817a7869f73c7540b5fdfe184b0be28624cc6ca9a01c52a140d4a2 DIST caftools-2.0.tar.gz 2644892 RMD160 29f389d0861f8c60efa137a53816abed5286214a SHA1 9ed7ed3d8be2bcde86aab8a79d4a61408cdc49f2 SHA256 b41f323ceb3fd260d6c2ecff1f285548f40301065cea54687eb96717534eaad9 EBUILD caftools-2.0.2.ebuild 1581 RMD160 bacc32349fcdcb76f6569db199385bd9fb51d6f5 SHA1 c5b411c13045623376779d615e310c4e375c0937 SHA256 3df664db4d5435f9b396fab721ec74cce26d997ced582028dbc662aac8d09b37 EBUILD caftools-2.0.ebuild 1068 RMD160 bdc6a4b5b423bfca1cf310f37db1f36ed5da9660 SHA1 0fde3ae97fda1cf06e2035e45f9cacefffa54c21 SHA256 613629e32ff2b43ca4f6ddc9428212542f1deccf69b868882a94ed20246d9e53 -MISC metadata.xml 531 RMD160 4e24b3b35b7b5399437676b65deb40c1533d7e15 SHA1 c0ac47f9d1d505bc7dddf2dbb5a2ef5e4905643d SHA256 8da1039b073c1c438b5a93089e469c9e35b7dc1297d6ac181e7d81809dee6049 +MISC metadata.xml 539 RMD160 811d93c4d63a12d2534865e7f848b41974c82a43 SHA1 5ddac4a5841b1c2e487f847d37e1a5e2dafa1c8f SHA256 84f5eb9ec596906c56f2e74dd64eba9d46895a45d1178e0b8c3bf7ff19bd8c36 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Ex5oACgkQgAnW8HDreRbRtgCfaasNnmY98tewV7p1jbGiD0F4 +zXsAoMEJI0ipeTsvrhxZ6PDwE/jEfrLr +=v2js +-----END PGP SIGNATURE----- diff --git a/sci-biology/cap3-bin/Manifest b/sci-biology/cap3-bin/Manifest index e93a18b35..3148a591a 100644 --- a/sci-biology/cap3-bin/Manifest +++ b/sci-biology/cap3-bin/Manifest @@ -1,4 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST cap3.linux.i686_xeon64.tar 430080 RMD160 f5a5e6643747b35de14fa2dab3f5b0d6756abc8c SHA1 b1e06785286f3509a8d08cd2e3400e2abb9e7888 SHA256 fd7112a89dd349e0d11820d4bfab34c3556eb570828f71a8db18b68bd6aa1c2c DIST cap3.linux.tar 409600 RMD160 a3e4fc661ac349791b2c9f1d5982d6b34f502122 SHA1 0de4f5de7fd3a4f6bae9d402f5bcd4937fe15ea2 SHA256 49916f0ac2dc7b6f28fd88e79f98eb097e059839bd9311593ef3fc6f77bc4648 -EBUILD cap3-bin-20071221.ebuild 1463 RMD160 cc06270e4c2e9fc0204296d552eb6f749a92c386 SHA1 ea015dee363244e53a16b771a161476e42ea0397 SHA256 b7adefe5ea1f7e31a9d3f7f420c3aa1bd7e3539bfabb2de884d562b3433c32a0 -MISC metadata.xml 391 RMD160 1af9555e8977c2e8b9bb8ba330498a8e5d050907 SHA1 0068e6453a108df09f7adb2875f61fec6c73140b SHA256 019499f4ccf9bcdf115a3ffff6af37bdf9a14ae2613d087f73149dfdc6eebdda +EBUILD cap3-bin-20071221.ebuild 1479 RMD160 2c2726cbb00ad6596b4c2b44824e342256bf5ecf SHA1 a1f5a59778f37c78b4c2819f89edff08c727fa1f SHA256 1268644cbc1d0ee100906fecb4debbc11b239c6c5ba40503e12f35f1ab938fef +MISC metadata.xml 399 RMD160 b4d8b61da12d50650bc9a7240664b2ccb11b4c3b SHA1 33c15e90cea2a4d530c4a4bc998bbad10f850edf SHA256 169911bbc957ca5de82f7f818e746c917a9698ade71b03d99e60a5912620c226 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Ey3IACgkQgAnW8HDreRZdKQCfcQFotsJkMbnzcnXjXdgeVlXy +XTUAoMigo6CG32wshx1VhQ/SgvaRIsr1 +=unOA +-----END PGP SIGNATURE----- diff --git a/sci-biology/cap3-bin/cap3-bin-20071221.ebuild b/sci-biology/cap3-bin/cap3-bin-20071221.ebuild index fadedf7a9..cc6f5e30e 100644 --- a/sci-biology/cap3-bin/cap3-bin-20071221.ebuild +++ b/sci-biology/cap3-bin/cap3-bin-20071221.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=4 DESCRIPTION="CAP3 is for small-scale assembly of EST sequences with or without quality value" HOMEPAGE="http://seq.cs.iastate.edu" @@ -18,25 +18,27 @@ HOMEPAGE="http://seq.cs.iastate.edu" # http://seq.cs.iastate.edu/pub/CAP3/cap3.linux.itanium.tar # http://seq.cs.iastate.edu/pub/CAP3/cap3.linux.powerpc32.tar # http://seq.cs.iastate.edu/pub/CAP3/cap3.linux.powerpc64.tar -SRC_URI="x86? ( http://seq.cs.iastate.edu/CAP3/cap3.linux.tar ) - amd64? ( http://seq.cs.iastate.edu/CAP3/cap3.linux.i686_xeon64.tar )" +SRC_URI=" + x86? ( http://seq.cs.iastate.edu/CAP3/cap3.linux.tar ) + amd64? ( http://seq.cs.iastate.edu/CAP3/cap3.linux.i686_xeon64.tar )" LICENSE="Artistic" SLOT="0" KEYWORDS="~x86 ~amd64" IUSE="" -DEPEND="" -RDEPEND="${DEPEND}" +S="${WORKDIR}/CAP3" src_install() { - cd "${WORKDIR}/CAP3" || die - dobin cap3 formcon || die - dodoc README || die - newdoc doc cap3.txt || die + exeinto /opt/${PN} + doexe cap3 formcon + dosym ../${PN}/cap3 /opt/bin/cap3 + dosym ../${PN}/formcon /opt/bin/formcon + dodoc README + newdoc doc cap3.txt # other examples # http://seq.cs.iastate.edu/pub/CAP3/data.tar - dodir /usr/share/cap3/examples || die - insinto /usr/share/cap3 || die - doins -r example || die + dodir /usr/share/cap3/examples + insinto /usr/share/cap3 + doins -r example } diff --git a/sci-biology/clover/Manifest b/sci-biology/clover/Manifest index 74679997b..d19acf301 100644 --- a/sci-biology/clover/Manifest +++ b/sci-biology/clover/Manifest @@ -1,45 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 -- -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - DIST clover-2010-02-19.tar.gz 15641 RMD160 aeeefc128976ce299e5ad65129cc0891104f0348 SHA1 ad30ac6440c6abfe53876ccc94149eec34e16b2f SHA256 f6de99b9ce5676af8b4179e12c4701f81f0b17ac5dadacfe7affa38ad2a585f5 DIST jaspar2005core 14913 RMD160 6fe43472cc1a2e0389ad9290801db56488773d3e SHA1 be8cdff62cf35f430c0c17f53564529b08000c9c SHA256 498a560c67411789106b50ccdfd9bc41f571d77c2fe9bfba7e95128c0a122fe4 -EBUILD clover-2010.02.19.ebuild 1068 RMD160 ee85f019c8e3914d41e7a902f1afd1b250c22b7f SHA1 056c74812ac0ee941c6975c706ad3e94c177a8ad SHA256 d13347e138e155e7d12588dfd15457510d2d8caecdf5f7bb26c82408572467f1 +EBUILD clover-2010.02.19.ebuild 1068 RMD160 33df8e6f80650fc17ce9d0fbda7d9ec318dfef7c SHA1 9763b5036cfc7feeeee887148cf962bf0404017c SHA256 514616a014b196e736d8f4b2f0f5b6df78ed4ab51498e92e05fa7d578f8420ce MISC ChangeLog 670 RMD160 76fec21f730ded591f166b128cee5ad87730e387 SHA1 45db195b3b23a9f0da9dc81a33a8f23303770faa SHA256 446dad253d4a186f03678f0aef1d9b6f0c683bb7390814c1c7b27ed7c829a2f4 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 -- -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) - -iQIcBAEBAgAGBQJMcsvnAAoJENwGBM22xffeL5sP/jDmo45oY5thDk+pt3owS+GP -jX5BnheYpo1yRarTGbkYHflROiV5tuXMv/lKj6WFft/OlVIZfVyx0lpcie+OAppQ -b3c3MOUOWRTQz4MYBZ/HbagJ3ArVWHfw3BArSI24lcsGfeMTxQt0E2TyCNNOnmO3 -HAR+KxaKKjdz3lKWPg1fVqbDYt+T6fhWtG8BcTONAzB72y78qYG7twKiO52AcWSp -sEGyK7RlPqduJmeX2yyzJQcQRnI1kq7/FjVuzcw470BXQe4S1MGlPvKim8QLyoti -1jh2Vt9hiSb4NLmothqEFs4dUwXOrclPzia1DfNJynCBFrhj3h/Qk4f+rIHLtp3I -IhiRLHEawZzJNdeUfMwDCY6IuwWi7H9gLpVeJSiYIN47baCuUVjQDZ0NTa0/wuHU -9IGyjn2XZGGzs9r/dJu3MVN8FJz/V+lmXKJQ/QPVJIjLosFM7yJBaeaPHKrAFlnV -u6rRkDzIgyoqLxdSUdMHxIDSgKoI5NvnA02dnCK/I2ANM/18ku1UoyKK1N8LJcTD -n8bAU4rWCt7+w+D1ltHeDvOa8eALT1aGGbqzJeAgtOZxp3USWwWj0wDG4vPb/SeO -VTaNV1OprAZ8eC3uV806RaXRXHAqvBkcyBJdle38RQOuBw4bJ3PkXQv3JON/WcSI -rZgPMzMkbwCkKnq9Ppro -=7fhm -- -----END PGP SIGNATURE----- +MISC metadata.xml 225 RMD160 281076a863af4791e194c7c0b39ccd572e95d0f2 SHA1 62bd67899a22705ac2475b479d5b31a331cb26bf SHA256 fd7f5bfdfd9dce3dd874edd9ff9fd12dcd83aba1c73b0c62399e8aba52e435fc -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.16 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iQIcBAEBAgAGBQJMcswRAAoJENwGBM22xffei/0P/14eh/3mDWL54PJMGPc38Wnv -nl7rJDdeZJf2LdjhgRGS7a1VoP34Jmg+TFwA1LHNhqEcuxQV7z4oQGi/HLHYI5i9 -64r1+agm+RIk9+VhGgf/r22y5v6ZwqzBN+SxC29mHvSJuwbjw+jHvJdqzhKSDkvd -caiFdE1oYwhGQ1qXiBrElTZkfprpaNwjwYRSOkyefj5P+FV7PFK3tzVsTq7m79Ab -pNHyIc9zTYI2YhyQ9v3jFJhGJsDb9JqoEwqYHLtPda+b7/ekpv4frLBgNSajKJeu -lHR6eVS4tA0WcCVnUHjCPAOJisCtOLQcao1c5ViftpvfofNs+BHtvmlBm7moPCvv -sAB8JVbzBIZ4rcFwy/7mjYe7MZ1MsmiLZR2D3X71K0LmRp5UgjjaJjczTUQ0Fqtg -9WbJOiDR7IPfxjhmfAZK4aeSnXD+rVjZ+MPOGRUuD2zplj9NuQK3PTgndCdI1Yo8 -jGSTkRNa5Civ4c2FEQW4UlCrKB+u35+ocyZsPniFkdP0hlN66eHfsOxIE562qaFU -GkSvN4HWiW5yS4fdEcGh8EM/ojUnRQN/2T9flkA+JHdhAy/+6+ilVv10pVlJ0Ala -af+rxjDbkPaeo+8kBYQvhSChVv84gQOBj72KSziBTmSgDWYXs4BFXPj3Pmx7Bwcr -+MSjiUj5Bhc185SjfZOA -=T+d9 +iEYEARECAAYFAk4Eh/gACgkQgAnW8HDreRY8tACgzJ1dGICxmztGGCVYJ05z+hba +QMEAoKTiqkCsI+B26uZICnG+Z4Vy9jla +=PGkq -----END PGP SIGNATURE----- diff --git a/sci-biology/clover/clover-2010.02.19.ebuild b/sci-biology/clover/clover-2010.02.19.ebuild index f14b70a16..239cc30e4 100644 --- a/sci-biology/clover/clover-2010.02.19.ebuild +++ b/sci-biology/clover/clover-2010.02.19.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -inherit versionator toolchain-funcs +inherit toolchain-funcs versionator MY_PV=$(replace_all_version_separators '-') diff --git a/sci-biology/clover/metadata.xml b/sci-biology/clover/metadata.xml index 7e3286984..9e64bf890 100644 --- a/sci-biology/clover/metadata.xml +++ b/sci-biology/clover/metadata.xml @@ -1,5 +1,6 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>maintainer-wanted</herd> +<herd>sci</herd> +<maintainer><email>maintainer-wanted@gentoo.org</email></maintainer> </pkgmetadata> diff --git a/sci-biology/codonw/Manifest b/sci-biology/codonw/Manifest index eb2e90af1..5802e4d51 100644 --- a/sci-biology/codonw/Manifest +++ b/sci-biology/codonw/Manifest @@ -1,4 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST CodonWSourceCode_1_4_4.tar.gz 161908 RMD160 9e01d48525e5308e8719f89276a12a3909d64a09 SHA1 a440d1ebdca328ed1f5efa7342267b7a2e764b3b SHA256 951e2a686f7849e0fa225b83b09842d4cf822ecafd67bff0438fc815512183b8 -EBUILD codonw-1.4.4-r1.ebuild 928 RMD160 06354dac3504df4e4feccf6cf6261a0c1c8a6dfa SHA1 acd84fdeef62f055a8cdf6a033edfe7f883d8f10 SHA256 c99157862f6ee0a30e0c62888ac9d9d5977eee9e12cdd4fd650801eac9824e38 +EBUILD codonw-1.4.4-r1.ebuild 928 RMD160 c8c1a14377188542889d6ede54538223ee865223 SHA1 d98279ddd25dba4cb8c1c7d55ef492e0c5bf7270 SHA256 382bd0ffef52b148657497df54f58be47081dc2165478dc9180711a14e39f295 MISC ChangeLog 435 RMD160 be5677fe4fe3cce0464834389b5c02e1dfb06ff5 SHA1 6318f550aa8e0f901ac5f3b57a52e2f404aeba0b SHA256 9d4201e4ff6acccc66c516e3a970b415a4820f167010fa8fd3dc11c5217847ce MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Eh/0ACgkQgAnW8HDreRb2gwCdEWq45ZAa7F0/PYnbNYE0DWSQ +t18AoLHX5NDr2XRfGcckk5HnSCY1JMPu +=+KUN +-----END PGP SIGNATURE----- diff --git a/sci-biology/codonw/codonw-1.4.4-r1.ebuild b/sci-biology/codonw/codonw-1.4.4-r1.ebuild index 3563ddfab..05ed6ea14 100644 --- a/sci-biology/codonw/codonw-1.4.4-r1.ebuild +++ b/sci-biology/codonw/codonw-1.4.4-r1.ebuild @@ -4,7 +4,7 @@ EAPI=2 -inherit versionator toolchain-funcs +inherit toolchain-funcs versionator MY_PV=$(replace_all_version_separators '_') diff --git a/sci-biology/consed/Manifest b/sci-biology/consed/Manifest index 73cf624e3..73899c6a7 100644 --- a/sci-biology/consed/Manifest +++ b/sci-biology/consed/Manifest @@ -1,6 +1,16 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX nLine.h.patch 237 RMD160 2fa26b40e186f5a5a840a244386484be17350edc SHA1 a842928142ca4228c8a94b1f7daca37ed77cc301 SHA256 376f61dbbd142b6927c2f0b1984d03499ad1e7ffc70b646bad46c5fe006e0350 AUX nextPhredPipeline.cpp.patch 439 RMD160 747bc2e640d04525e9e085e4aa33bc45ad1c3eb5 SHA1 5d658507a91af26fe4477608aeaf6db87bd6bc27 SHA256 3ac55169665cc74507ea5f405a67d43a37a3d2733d74b877f732674c4e2e8e82 DIST consed-20-linux.tar.gz 31407408 RMD160 8ab84f5216bb433884c75806738a6f7f20dea915 SHA1 9ccf1a2db890e30f042188d20e52098e1e37987a SHA256 ebde602163743d018ac8bf49f04ff0afbd0cccb3b7ef065a154943a68e95ad27 DIST consed-20-sources.tar.gz 7418118 RMD160 2dafda72027ecefd20333bddcec0b3e24d102412 SHA1 a222ef3a34c4940eabc8e0250ae88a86c5ee27b5 SHA256 8d12191e08d9dfc73c3284a057b7fd80d1aefe4a60d11a0de1db6ba9ce9ba4b7 -EBUILD consed-20-r1.ebuild 2495 RMD160 2a1832e72bbea1b782cbcea2cc98053dc3fbcbc6 SHA1 81dd87503c95c853464f6ce4100e8f8d3f499136 SHA256 7a84e27608e40ff07e49c488ab7d9754d30ff376541617ca5a529010708e9ad1 +EBUILD consed-20-r1.ebuild 2495 RMD160 41aca137feda9859a997dc2c8adc04790231bd76 SHA1 37228fa4128d4f091384d821f63001df368c275e SHA256 f7831b85683c057afbd48d7830147aca7c2f6d8e03485477948e3b323a9686ec MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EiAIACgkQgAnW8HDreRYZQgCcDET079yuAcbfOjok/M99Uvzw +Sk0AnRGjhAhntG3bxr5+HuCAWTJZ8h44 +=X0Ic +-----END PGP SIGNATURE----- diff --git a/sci-biology/consed/consed-20-r1.ebuild b/sci-biology/consed/consed-20-r1.ebuild index 5c65e660b..0ddce15bc 100644 --- a/sci-biology/consed/consed-20-r1.ebuild +++ b/sci-biology/consed/consed-20-r1.ebuild @@ -4,7 +4,7 @@ EAPI=3 -inherit toolchain-funcs eutils +inherit eutils toolchain-funcs DESCRIPTION="A genome sequence finishing program" HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html" diff --git a/sci-biology/dawg/ChangeLog b/sci-biology/dawg/ChangeLog index ff3e5fed1..ad8b3b952 100644 --- a/sci-biology/dawg/ChangeLog +++ b/sci-biology/dawg/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/dawg -# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: + Fixed herd entry in metadata.xml + 24 Jun 2008; weaver <weaver@gentoo.org> +files/dawg-1.1.1-gcc43.patch, +dawg-1.1.1.ebuild: New package diff --git a/sci-biology/dawg/Manifest b/sci-biology/dawg/Manifest index bac910e38..7c2b7c109 100644 --- a/sci-biology/dawg/Manifest +++ b/sci-biology/dawg/Manifest @@ -1,5 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX dawg-1.1.1-gcc43.patch 251 RMD160 432f37ab9d976958161cc05c8176aefca2d34047 SHA1 aa560bc5086e8ef17437d23d091be46044080f63 SHA256 85ac21adb231fa971d11597dc9e5f3725a7900889841e6665119ac1bf807722d DIST dawg-1.1.1-release.tar.gz 213877 RMD160 d2be74cf13c5aecb30cc08f4404d954f6f4272c8 SHA1 fe2942ab9d73d22fd02a8dd06bd8874b7470d487 SHA256 dd621d7913fc1511b52ed2bdc5856e1e591464ddf8ee5c2e7eaa45ac81705286 EBUILD dawg-1.1.1.ebuild 607 RMD160 7832fc450b66ec3763bca33070ef6f6573f813c5 SHA1 c2b987a3e3c2a001eedf4fe01a265aaacc30a087 SHA256 33421468781252e7fff1a238b0ca30c7e2be9c433985e70986e82c5597866333 -MISC ChangeLog 227 RMD160 56af05e22cc08ee72a7bd7e75ab928b3c9e07e6a SHA1 83e5a13bbdd76547150cf934ae0ef2a043d18767 SHA256 3ae2b976f9eca9d456a198f01294bb489a03096c49021212216798be97b5cfd9 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 +MISC ChangeLog 324 RMD160 fa6ced37eca55f0a9b6a3009df761e83e59938e0 SHA1 d4f71cc8ba5e0f9944d181fc3d94e73f49e17f77 SHA256 7632e828e8ff7464d35516a70ee32cdb99e6f2d8956c88dfdb1565ce37b09ff6 +MISC metadata.xml 158 RMD160 9b441c987a00c5a66c06850c0d587a2abd70893c SHA1 7a8997eb2fc55fda167d3e95cdffb43c8f817fdf SHA256 dae7918daac89b300804812d32584889aa1c4e8b9edeced06006900494457a6d +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4FkaIACgkQgAnW8HDreRacngCcCzOtR+z/0GLQ5EFv4EnHQT2r +gbIAoKQnApG+KCVRKqKuAig2S0IuvX3o +=fw2v +-----END PGP SIGNATURE----- diff --git a/sci-biology/dawg/metadata.xml b/sci-biology/dawg/metadata.xml index 7e3286984..897aa2e6b 100644 --- a/sci-biology/dawg/metadata.xml +++ b/sci-biology/dawg/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>maintainer-wanted</herd> + <herd>sci</herd> </pkgmetadata> diff --git a/sci-biology/embassy-cbstools/ChangeLog b/sci-biology/embassy-cbstools/ChangeLog index f4ed9e2c6..5588b77aa 100644 --- a/sci-biology/embassy-cbstools/ChangeLog +++ b/sci-biology/embassy-cbstools/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-cbstools/ChangeLog,v 1.5 2010/01/15 22:44:35 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> + embassy-cbstools-1.0.0-r2.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 19 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-cbstools-1.0.0-r2.ebuild, files/embassy-cbstools-1.0.0-r2.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-cbstools/Manifest b/sci-biology/embassy-cbstools/Manifest index 4bd6e4a83..095dd6797 100644 --- a/sci-biology/embassy-cbstools/Manifest +++ b/sci-biology/embassy-cbstools/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-cbstools-1.0.0-r2.patch 9656 RMD160 152ea616559e1d8377267ae6e5d8035e525e6e19 SHA1 8974cde7df8b76c99551760a93bd007211993986 SHA256 79a0b8fb574fe2d55bbcd8fca7ef2822c3c7e1e573565996c3656645f3b41845 DIST embassy-cbstools-1.0.0.tar.gz 389856 RMD160 019d278d482c621c1cecf75dac99493168a5de65 SHA1 c16abdf8c3d5b8a4e31fdcd20a556f35bdd671c6 SHA256 fd1c6a5f588d548791c98d2c31841705ac6971163a7f95345542932960080b5e -EBUILD embassy-cbstools-1.0.0-r2.ebuild 383 RMD160 dd1457128ca42fb18d433650407f1debe4db1c48 SHA1 2a17d9167f913f6c53c8e5516a7ecba656ff749d SHA256 ed41ac5a77816c74b339ce80d3cea9a8edea0489a81aadc95925f5c3d188ff36 -MISC ChangeLog 1522 RMD160 9f1b5c8d47838c8764bf60677f0ce1e790192307 SHA1 bece2c6805129a8d404aad819da50c0749bf8fec SHA256 18976a4da34e830371ca4740038094e538e6b6401f5042c6c195ee9df871bb2f +EBUILD embassy-cbstools-1.0.0-r2.ebuild 378 RMD160 279ff65e206230320b07b33d1cefe89341f2c152 SHA1 1dcee934c0e4b6009f0fba68622f7d3221808298 SHA256 a210592d8effa9a3c87000434bb7c083a2a697d5439b169bc9141464510504b5 +MISC ChangeLog 1675 RMD160 27a45eefb1bf4e2be1de18428b6dceb184ee5c01 SHA1 d214a352d09171307ca3dffdcf1f0e229e7daff2 SHA256 7d7467dc1a93ef7f0093ab1c988b47f7ddc720c344776783fe7b3dc9a463ecc0 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2EopUACgkQgAnW8HDreRYUtwCdFuOfcGcCw2mPkyk8q6w+PwiV -en8An2GIRROpmUwVBJKfBU7WYMPAKHo8 -=K1MY +iEYEAREIAAYFAk4GAa4ACgkQgAnW8HDreRaMxwCeLAXLPbDyAloWfdMalhLVUIaa +Lv0AoIyXED7qXOduh+ylvlzKOZNzty+m +=gIH2 -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0-r2.ebuild b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0-r2.ebuild index 4642b30c7..78c619eab 100644 --- a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0-r2.ebuild +++ b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0-r2.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="applications from the CBS group" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-domainatrix/ChangeLog b/sci-biology/embassy-domainatrix/ChangeLog index 819cf4f6b..9377854f3 100644 --- a/sci-biology/embassy-domainatrix/ChangeLog +++ b/sci-biology/embassy-domainatrix/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domainatrix/ChangeLog,v 1.29 2010/01/01 21:48:13 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> + embassy-domainatrix-0.1.0-r5.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 19 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-domainatrix-0.1.0-r5.ebuild, files/embassy-domainatrix-0.1.0-r5.patch: diff --git a/sci-biology/embassy-domainatrix/Manifest b/sci-biology/embassy-domainatrix/Manifest index c29621bf6..a93e8fe43 100644 --- a/sci-biology/embassy-domainatrix/Manifest +++ b/sci-biology/embassy-domainatrix/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-domainatrix-0.1.0-r5.patch 9588 RMD160 51633db082a16f45274fb96371e6a384ce3a2fcf SHA1 afc886fc9f34cb71a66f2f09f3dd5b3ed3a448dc SHA256 818d81968350bae8d0492e4103ef7d4f41dd651321735c5d5dc04f4b35bfb8c4 DIST embassy-domainatrix-0.1.0.tar.gz 426218 RMD160 da6136665c4e951a6ca93362692fc299be2c05d2 SHA1 b7c9d14203fb1e9fff2fb7608c8edf87a346c133 SHA256 f6afe128cfb42dac7e734e979910d3bc7dd879ad1a677012f12f33572bd70989 -EBUILD embassy-domainatrix-0.1.0-r5.ebuild 383 RMD160 bc0f0c1b39241e06bd6a95d2859b0d2d4845bba3 SHA1 cbb23311c6b95338a5f9729e1ce4491406d19c62 SHA256 0ea008c9157a53bd78955754df81048975f887d1b06fac2b3e8c651046c68d06 -MISC ChangeLog 5357 RMD160 bc43bd64d16b91290adefb005d01ede07fd679fa SHA1 8ff260f7a1c872f443de4c2891d178875883a08a SHA256 6c12cccf3481e054a7aa36b84c96286c13ad236ba560481a3bf3a032eafaf691 +EBUILD embassy-domainatrix-0.1.0-r5.ebuild 378 RMD160 d8868e7626926173256b56b2fb638d454866b3e8 SHA1 b0a505534e84fd6c80b5b421987b577d71b7fbff SHA256 d01a3257f3af0d6b4fb47585634e3a188d7b7fe19f43c240e9c04f2c122a9895 +MISC ChangeLog 5513 RMD160 31a6d5ce03f35c9710701a5db981355b2c14e69f SHA1 2af219fff22fa4a1dd718adc4da9dd99335ce936 SHA256 af41911a9f76481c9b90f39bc24f3d4ca81a8893dde7093268a83944aacc66ed MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2EpJYACgkQgAnW8HDreRapUwCdHO/9eJaP+C+s1nkSG/k/Izsb -MS8AoIOouBCvYaN7202LceJGUXF2QP+P -=6j4K +iEYEAREIAAYFAk4GAcUACgkQgAnW8HDreRYImACgwoi57Dmd7C/3RU95IhaMwIYe +eAMAn00tr+YqkE7Ra8IluzEMxzuxo/6W +=15FX -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r5.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r5.ebuild index 9ba3995ed..8892a8061 100644 --- a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r5.ebuild +++ b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r5.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="Protein domain analysis add-on package" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-domalign/ChangeLog b/sci-biology/embassy-domalign/ChangeLog index 5d5d4cdba..171f1a209 100644 --- a/sci-biology/embassy-domalign/ChangeLog +++ b/sci-biology/embassy-domalign/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domalign/ChangeLog,v 1.20 2010/01/01 21:51:36 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> + embassy-domalign-0.1.0-r5.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 19 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-domalign-0.1.0-r5.ebuild, files/embassy-domalign-0.1.0-r5.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-domalign/Manifest b/sci-biology/embassy-domalign/Manifest index a4bbcaedf..10e364c4b 100644 --- a/sci-biology/embassy-domalign/Manifest +++ b/sci-biology/embassy-domalign/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-domalign-0.1.0-r5.patch 9586 RMD160 60830ec72285bdafd6e36a3667bf9c8f38aa4796 SHA1 89516869d482d4a3540bcca8fda28da063478b0a SHA256 551e01c1c91596e9f8454e6a53015edca265d0d22eec3ec6e675c6e49eeb2b87 DIST embassy-domalign-0.1.0.tar.gz 441025 RMD160 ba356997be2baa4c526740f52f65d4bc016461ca SHA1 5260a40297f43633e68e1577325275b0a196c60a SHA256 345db267970cb9a8c9c41f53a5063185d36d13bf61dcc8941569d9bb2d18c567 -EBUILD embassy-domalign-0.1.0-r5.ebuild 378 RMD160 d295d835790077174b267bcd375ea18558704e94 SHA1 624c3144ed9ac1020e2ddd793431a26a9d707d7f SHA256 9d53dc57f4025cd13a56ad835bd48efaa5f36af6392454b83723ecd8ff05b684 -MISC ChangeLog 3495 RMD160 69c9e2bf25d7510826059ea6eb02e411259940ec SHA1 d8c9eff4cf959d5e15806ae97bffb5d83dee4868 SHA256 1451fbc4949551cbaae77e1170b64ac12ad34227c94a4a777b794b056c60d72a +EBUILD embassy-domalign-0.1.0-r5.ebuild 373 RMD160 5c7e9a075f2b32e7c7ccdec112354742dcfa7a4b SHA1 43eafab9510280266add0d43cced378049c697dc SHA256 e44e64c7c79ba070270d9237a7a2d39d854e2d248c4fd7ab5486bbd319523518 +MISC ChangeLog 3648 RMD160 0aff0ada60e9ed7285f83ab5707f417bb890abef SHA1 13492eae0cbac60e10675c866fe0acc663a0e76c SHA256 3e704961800746684e8c2407b04a7155ad79523850ff0030ea86e47cb4d94b6e MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2Ep5gACgkQgAnW8HDreRY9/wCgyI/ZyvRYyUmTG/brxelHWhRM -FwUAoJE4IT9Yxj8XTgKYZ5RhIekpoRPT -=3Dze +iEYEAREIAAYFAk4GAdgACgkQgAnW8HDreRafSwCfSiAnnJawmlZ2G25XOHQzl0ZF +ThAAnjsXPG3PeC6qzPWdorU18vwM2IkC +=UGgf -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r5.ebuild b/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r5.ebuild index b1d116394..4751d1fd8 100644 --- a/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r5.ebuild +++ b/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r5.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="Protein domain alignment add-on package" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-domsearch/ChangeLog b/sci-biology/embassy-domsearch/ChangeLog index 5a4cb2995..e206e653e 100644 --- a/sci-biology/embassy-domsearch/ChangeLog +++ b/sci-biology/embassy-domsearch/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domsearch/ChangeLog,v 1.19 2010/01/01 21:53:24 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> + embassy-domsearch-0.1.0-r5.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 19 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-domsearch-0.1.0-r5.ebuild, files/embassy-domsearch-0.1.0-r5.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-domsearch/Manifest b/sci-biology/embassy-domsearch/Manifest index 149bc5139..2fa7e0c50 100644 --- a/sci-biology/embassy-domsearch/Manifest +++ b/sci-biology/embassy-domsearch/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-domsearch-0.1.0-r5.patch 9557 RMD160 b4af6f43b44fd408e867034309c21a1fd847b3f4 SHA1 e4a20f94557dcda2ef3533e60c7c4b7b2e1c97df SHA256 4c69c017bc435c3aaedee62238d643d93c749344f1a0c6d3776ff890cb3c0afe DIST embassy-domsearch-0.1.0.tar.gz 452787 RMD160 3a3b58bd700e1b4cb4ddf78ca944f9fff12262df SHA1 2f85959b2fe7314372d23b5f993af2a174a85997 SHA256 8f64eae467246389306196847f3428e848628a0b6e051d54bcf4659595f4aa75 -EBUILD embassy-domsearch-0.1.0-r5.ebuild 377 RMD160 28a9f1b73e72d6c6a9e92586bb070af2b04c5e10 SHA1 b090777e23aa2121dc339581fa6cd6ac7f2c1433 SHA256 d4c09ce57950316c31825f4bdb0a4d27192bbe74cd11ab2e14f3e57019a7c60d -MISC ChangeLog 3432 RMD160 a279f1c1029b4993c8834d34930576c61848a3a2 SHA1 a4aba7565e390d5508c94b30c9360522fcbc7cc7 SHA256 943be6cb1a1dd33a7b16ccf736e4013c73299c04530dc2287235f980d8517ff0 +EBUILD embassy-domsearch-0.1.0-r5.ebuild 372 RMD160 32b82d2df1c34e131172251b985b6dd455d51951 SHA1 1e1ec3fa74cf64b65ad0e29fbe0ba9690c4e7f56 SHA256 0cb78f65aa00dd4a6160647b4c662e83b2fa8c5916b1ddd99f2b6b492fbcfcc1 +MISC ChangeLog 3586 RMD160 c19f6c3613d5b6b62538370346f4fadb48ae9b19 SHA1 27e8ba66d9601062b45ee52412332546c2ebe9ad SHA256 55035e184a7bacaf580222538854d055e58b3885664b56e876c926573197ad32 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2FBfgACgkQgAnW8HDreRYKMwCfcj7s7+X9tk/vW9BydpnDyM27 -Hb8AnRLbC9ouyjwoTMeaOeN5ru6BJfLk -=Tx4K +iEYEAREIAAYFAk4GAh0ACgkQgAnW8HDreRb/1ACfUmPO6RawkId8RnI8aKqeGmr9 +huwAn2pionTN7GsFtH7XUJGUm388DkMq +=z4Ki -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r5.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r5.ebuild index 3deb535d7..56e828ce5 100644 --- a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r5.ebuild +++ b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r5.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="Protein domain search add-on package" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-emnu/ChangeLog b/sci-biology/embassy-emnu/ChangeLog index 6334ae1bc..94f00fd9f 100644 --- a/sci-biology/embassy-emnu/ChangeLog +++ b/sci-biology/embassy-emnu/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/ChangeLog,v 1.29 2010/01/01 21:55:20 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-emnu-1.05-r7.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-emnu-1.05-r7.ebuild, files/embassy-emnu-1.05-r7.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-emnu/Manifest b/sci-biology/embassy-emnu/Manifest index 176a2067b..5a09c1d7b 100644 --- a/sci-biology/embassy-emnu/Manifest +++ b/sci-biology/embassy-emnu/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-emnu-1.05-r7.patch 10038 RMD160 4cbbe9c049346f8dddcbb0e2663a5a6bcec7eb85 SHA1 9c5970fac281da1bcd301f69bb1eda3f0e558b46 SHA256 ee578534c253c43078a03b7018b686157e9ad695dae654549a66348a46a12db7 DIST embassy-emnu-1.05.tar.gz 373798 RMD160 9844ed22591a7ee857920f2fd4eee5626de39ba6 SHA1 8c8781cf48a8d95aacc452d1edf5e77144a34987 SHA256 70568ed4f68c174706f17df27cfb3db05c9e0e0d3cf42029ea4fe96328588ca6 -EBUILD embassy-emnu-1.05-r7.ebuild 469 RMD160 311fc0e38196ab39662202405df455ec5b35849a SHA1 72866f2913cbbe147748902ca4dff070ecba83fc SHA256 69e268026d4b3efc10ccd6e5dac655338227e22f214cd85a92b3733a3130ff73 -MISC ChangeLog 4756 RMD160 f0db438642e887a45f7299c2f54efc7aaf13ba16 SHA1 b01fe739268f8f0882459afec6c6d54e3ef49803 SHA256 b409401952b3b7c483e7ed704c4bb13e639e7b869f2da6967df5bb8b7b81a574 +EBUILD embassy-emnu-1.05-r7.ebuild 464 RMD160 840d4d0699b90c315537e9262d1e8eb1739fe11a SHA1 aac132dd4babd270bd625931053259bdd70011cb SHA256 7bb1e373c7705f203e014dfd046081a94cd411e1da9b6c75eb0ab9f80c24caf1 +MISC ChangeLog 4902 RMD160 42e8d7ff1bee5eb0b5d22a1dacf08f4477cc350f SHA1 0bcdb16f557a205d33cfe64507a97ba630641cce SHA256 5272ed4038aa5d624fe95ebb88a702c96b15ec842c6cadb509070497df81de5f MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F4lQACgkQgAnW8HDreRa/MgCgi09tcMG3fsvH50XVyDAoMGRb -p2wAoLOl5ylsIuxOCUTIkdeCMGeCnRBk -=G5AP +iEYEAREIAAYFAk4GAj4ACgkQgAnW8HDreRZBbACguK+C+YhKqKyR5oGGy73cXRIf +xhgAoJAaFZvCpigtqzCjpEbd/yuVHbU6 +=R9Ct -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05-r7.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05-r7.ebuild index 0bf55dc39..f4538cdf2 100644 --- a/sci-biology/embassy-emnu/embassy-emnu-1.05-r7.ebuild +++ b/sci-biology/embassy-emnu/embassy-emnu-1.05-r7.ebuild @@ -9,7 +9,7 @@ EBO_EXTRA_ECONF="$(use_with ncurses curses)" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" IUSE+=" ncurses" RDEPEND+=" ncurses? ( sys-libs/ncurses )" diff --git a/sci-biology/embassy-esim4/ChangeLog b/sci-biology/embassy-esim4/ChangeLog index 0e7dd091e..5629297ac 100644 --- a/sci-biology/embassy-esim4/ChangeLog +++ b/sci-biology/embassy-esim4/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/ChangeLog,v 1.28 2010/01/01 21:58:14 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-esim4-1.0.0-r7.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-esim4-1.0.0-r7.ebuild, files/embassy-esim4-1.0.0-r7.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-esim4/Manifest b/sci-biology/embassy-esim4/Manifest index 7632db279..65a511896 100644 --- a/sci-biology/embassy-esim4/Manifest +++ b/sci-biology/embassy-esim4/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-esim4-1.0.0-r7.patch 9399 RMD160 34b108e0ad6ee283ff8c5752fce3225ffbf16091 SHA1 d104d8d4c84ab4ac80e28df25ce8310c1ee04d33 SHA256 42277736c23d9bb66ef7033447b5509f8313293727661acc17cd53f4fef38ece DIST embassy-esim4-1.0.0.tar.gz 415096 RMD160 9043eaaed74aab481b1a2e690a06932211421003 SHA1 76a2ea556a23241d94e17fdfdcc05bfa17dd8bfb SHA256 7abd69516d6e12ae58f568662db3bfa19bb3a15c03413db61ecda3f013b144f5 -EBUILD embassy-esim4-1.0.0-r7.ebuild 373 RMD160 a4b8e7a9425af8f41894f024b581529a9e65d76c SHA1 7844efd50e9002306cd98e8c0040f89a349aef3e SHA256 967f831aeac261c52c9bb7e217b32e64423180b419d115e04bd743da4f57dfd3 -MISC ChangeLog 4746 RMD160 a81634edd5ce8167ff9dd4748157359cf36ba7f6 SHA1 00a37eae5e7289b15a55629d70442c549bcc94d6 SHA256 cbc4902a8864403323771479866ceb373d61edf8d2f112a1139dae37a5e57c20 +EBUILD embassy-esim4-1.0.0-r7.ebuild 368 RMD160 69787846d2661b4267346554a6d65335f32245c8 SHA1 2140b8b390d30e8b08803e876b5f623a89a3d308 SHA256 4ca9027576eeb78a49cc6ce8c35ca5f8ba5caaf925bd82f6cdf39ee13568363e +MISC ChangeLog 4894 RMD160 6fc8d939262883ed53ee63f506afffa89eaa0773 SHA1 ea898c2ee001a0ce17b43645916839ea4aa0a241 SHA256 89674c146a18b749f9a0dd0ea7b6d665c89daf03cada834e981e9629b096cb30 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F43oACgkQgAnW8HDreRYTyQCghtcrpiPBAeGNUfKJwSvSfxV9 -GAEAoIMuWbUohsePxwyN2TsxrAVpNkLJ -=INXE +iEYEAREIAAYFAk4GAlMACgkQgAnW8HDreRY9pgCfQOorfDkF+7V+EqLAcTcJ2/9v +WAIAn2blUNlwv3Zioel2YOMVxpi6ZV9q +=w9ca -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r7.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r7.ebuild index 3662f65d5..eba377747 100644 --- a/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r7.ebuild +++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r7.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-hmmer/ChangeLog b/sci-biology/embassy-hmmer/ChangeLog index 3979e4956..a24cbb09f 100644 --- a/sci-biology/embassy-hmmer/ChangeLog +++ b/sci-biology/embassy-hmmer/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/ChangeLog,v 1.30 2010/01/01 22:00:05 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-hmmer-2.3.2-r4.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-hmmer-2.3.2-r4.ebuild, files/embassy-hmmer-2.3.2-r4.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-hmmer/Manifest b/sci-biology/embassy-hmmer/Manifest index 2527c1aa5..0382f8de2 100644 --- a/sci-biology/embassy-hmmer/Manifest +++ b/sci-biology/embassy-hmmer/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-hmmer-2.3.2-r4.patch 9564 RMD160 01329277e61caee71a6ee2a2cce0645c87e62883 SHA1 da160acedea05872176894c3a95388cbaa66582c SHA256 373996ef3b99630663b0e414386f540548ac643be980fc724d87c0efdd7529d6 DIST embassy-hmmer-2.3.2.tar.gz 569581 RMD160 1c2fdbe0b2aa4e5d3de45d9177c9ae9833acc352 SHA1 0ec9d34dc2a137b5c1b21102bebbd5c28354ad37 SHA256 d4c5ec18f9bdd049be7de138d4c560b4bcb39d9a239f791c6713c0857ea29c89 -EBUILD embassy-hmmer-2.3.2-r4.ebuild 438 RMD160 687dc9e50b82233fa54fe00a201b669c4a9ce039 SHA1 1dce6dec2ad24058158a7ba25e239f64b3bae28a SHA256 4a4e3517749e22a9391a522e4c179dc267d3f8ce312af968a91be8d0c5bbb441 -MISC ChangeLog 5028 RMD160 e55d0237d1181f01a505a27f65034e05bdd65e43 SHA1 1a6f1389f199afdf4741d26e923c940340944b33 SHA256 5dad8124424a0617675d57285fc2a389894da746fab85dc4a2f57b06da465912 +EBUILD embassy-hmmer-2.3.2-r4.ebuild 433 RMD160 3d098505f659369304d1dce8dca1475e5b195659 SHA1 307187135386efbe5bd3c8616f399bf5d87dbaa6 SHA256 ad44710230173dc05223ebc54caf3570ed4eb0e453510d8243594e4310466c8e +MISC ChangeLog 5176 RMD160 e046cd5b3cfdd827839187a496869161edb50dfb SHA1 4622688dcdcaec5b716c6144b87201b60aa1d147 SHA256 86ccd8f23cf30d2bb34cd694b2042f25f5753cfc3ae77ddf1ffaa6103dc4e557 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F4+4ACgkQgAnW8HDreRabeACglncH/YihlwLPOuQj9WyqYb4r -/hUAniEEoL3cwAnF4uAtYE+Vt9itufGQ -=fuCH +iEYEAREIAAYFAk4GApMACgkQgAnW8HDreRauAQCeJHSZh6ySOVS0aq8FMjVfZhM9 +8B0An1Evv0Em8C8XgwOw8CgBBJ5ggSUZ +=x0WC -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r4.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r4.ebuild index 6bbdf10e9..21de3d660 100644 --- a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r4.ebuild +++ b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r4.ebuild @@ -8,6 +8,6 @@ EBO_DESCRIPTION="wrappers for HMMER - Biological sequence analysis with profile inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" RDEPEND+=" ~sci-biology/hmmer-${PV}" diff --git a/sci-biology/embassy-iprscan/ChangeLog b/sci-biology/embassy-iprscan/ChangeLog index 5a00be37c..4bf1c83ff 100644 --- a/sci-biology/embassy-iprscan/ChangeLog +++ b/sci-biology/embassy-iprscan/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-iprscan/ChangeLog,v 1.5 2010/01/15 22:45:28 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-iprscan-4.3.1-r2.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-iprscan-4.3.1-r2.ebuild, files/embassy-iprscan-4.3.1-r2.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-iprscan/Manifest b/sci-biology/embassy-iprscan/Manifest index 16e26b40f..d2399b2b3 100644 --- a/sci-biology/embassy-iprscan/Manifest +++ b/sci-biology/embassy-iprscan/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-iprscan-4.3.1-r2.patch 9581 RMD160 18a520e521ab8b71cf00085bcb98c4ecb7831da0 SHA1 91b9390317f08f92106c6d22b1d0928ff9d9f3f4 SHA256 b0a36e2aeaef63533b51ef04ca5837fbeb21a4a98b7918495ee9915d2a1012a7 DIST embassy-iprscan-4.3.1.tar.gz 350791 RMD160 d92db63278c489cab73e47634021f057437b89d7 SHA1 e69e55d296b518bab97de21c4dcc10e113dc6ada SHA256 07b1fcfba00af74387312ceaadd890e4ad1af0fdeba4055c88d3d02dc64ee9ca -EBUILD embassy-iprscan-4.3.1-r2.ebuild 393 RMD160 c76fa1ffee5ba0af4fc224ebce59340dafde43b6 SHA1 9e2df1f415d065b5c386f8cc6adbbc99cff5848a SHA256 74a7a65ddc2593788ae1ba53e4f741bfce82a8f1da6d0927572f64b9c4293447 -MISC ChangeLog 1290 RMD160 aca04cd3cd6daee9873104a7bd7d96f967af71cb SHA1 0de1c10fc6ef68b0fc7b24bc987ca7d66de299c1 SHA256 545403fd49e98854da59f8ce52155a80da3a6d9d3989b752618e3b0aae5fd665 +EBUILD embassy-iprscan-4.3.1-r2.ebuild 388 RMD160 326aefc3b8b4b99bdfd27b5f21f42fc53b2f495c SHA1 71879e420064ee8e254e69f12b2ba223cb396de4 SHA256 a30a1ebad4eda4c68ae5bbb6ef31efd715907324dde38581e2437b1965cdde14 +MISC ChangeLog 1440 RMD160 95d8c31977f5018f02daf493896ece827ccc26e2 SHA1 2ec5225cb22266d3061859f750e7ad4fa28981e8 SHA256 30a2f848abb8d7aae9984412ba0d4c38dc62e5d10cb13cac0c862fe8d2017a7c MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F9D0ACgkQgAnW8HDreRbzsgCgw1Gt3VHE8mbtLmpw8744iUEr -sNkAnjbD1vxqf+kaT8vAoutaDeso0POG -=+azL +iEYEAREIAAYFAk4GArkACgkQgAnW8HDreRbNmACfcZdkfUT73Zf7+HFe4uzWpkCb +ejQAn1QO0sjxSlCm9UnQYV/+0dM4uEFa +=pE3G -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1-r2.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1-r2.ebuild index c69c12518..90b800037 100644 --- a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1-r2.ebuild +++ b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1-r2.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="InterProScan motif detection add-on package" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-memenew/ChangeLog b/sci-biology/embassy-memenew/ChangeLog index ed3b3d9a7..aabfabe81 100644 --- a/sci-biology/embassy-memenew/ChangeLog +++ b/sci-biology/embassy-memenew/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-memenew/ChangeLog,v 1.11 2010/01/01 22:03:00 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-memenew-4.0.0-r1.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-memenew-4.0.0-r1.ebuild, files/embassy-memenew-4.0.0-r1.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-memenew/Manifest b/sci-biology/embassy-memenew/Manifest index 03273a037..ee13424ad 100644 --- a/sci-biology/embassy-memenew/Manifest +++ b/sci-biology/embassy-memenew/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-memenew-4.0.0-r1.patch 9463 RMD160 20ff4a767e97e953877f9d37f99dee1eac9d45cc SHA1 df9e617534516f5718cbde59e410335949a18925 SHA256 1146c80e4ca91ef9c245b8f7a40be18b399e7c3d84a5cc8573c930832b4083ab DIST embassy-memenew-4.0.0.tar.gz 513418 RMD160 7072d182479a726e568b0bc2a4c7757ed1c6c087 SHA1 d382f39d1302f1b0799d5b6cb02cd9cfbecee972 SHA256 2192d33b5ee1147742f51416b0504812dfeb13b3b8ec0bfb62fd729e703a19c3 -EBUILD embassy-memenew-4.0.0-r1.ebuild 374 RMD160 62df7bc95f5c641cbed4c4974204850d0d50b8e4 SHA1 0e92818381e83cabf6c1aee7a6ce03c5c6e054e3 SHA256 f866cb71fff542644feef2ee276178cc8f6525087d6e34c92734d74a5e48cec2 -MISC ChangeLog 2082 RMD160 e72ab8d451eef69164411a24d3f9c038f710b3bf SHA1 bb0e0adb92139641df2657519c3d98267ae1256b SHA256 475b7025ccf640ed4d55647657ac28d8f92d55feb87266b6ea9a042d5cd8cdad +EBUILD embassy-memenew-4.0.0-r1.ebuild 369 RMD160 d54ebb68ddb2c73b8d79f11a9975e17a02876aeb SHA1 9638bb3bd6d16f48c8347581691a1efd69b7e2da SHA256 c437d23c97bca6ed61d02a9694d23c3e96d39f2701b50efcd4a75f2832f1e1fe +MISC ChangeLog 2232 RMD160 600b4b0585825d38dd1d8f1ee7650e59a200b657 SHA1 ac1be46f939ecd1b3df9e399226ca880779815eb SHA256 a95ade39fbda61bdcf24ba3736e80d95b053cda4bd9787cb8c8adc76b6ca9446 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F9aEACgkQgAnW8HDreRYC7QCeJGvbS5ghAizYSzH0sX4BqCDb -opgAn2ypusu9HZWVtMlibmd04yvcdIwV -=wUKc +iEYEAREIAAYFAk4GAt4ACgkQgAnW8HDreRYIzQCeMASsMM/k4TrLsaYIGCaIsc7O +lhEAoNMHBdobQy5oiLVJCYMR1gwU8qQF +=CJlw -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-memenew/embassy-memenew-4.0.0-r1.ebuild b/sci-biology/embassy-memenew/embassy-memenew-4.0.0-r1.ebuild index 1bb7a8f21..caa114b63 100644 --- a/sci-biology/embassy-memenew/embassy-memenew-4.0.0-r1.ebuild +++ b/sci-biology/embassy-memenew/embassy-memenew-4.0.0-r1.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="MEME - Multiple Em for Motif Elicitation" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-mira/ChangeLog b/sci-biology/embassy-mira/ChangeLog index 3376be216..18606d7b2 100644 --- a/sci-biology/embassy-mira/ChangeLog +++ b/sci-biology/embassy-mira/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mira/ChangeLog,v 1.5 2010/01/15 22:46:25 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-mira-2.8.2-r2.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-mira-2.8.2-r2.ebuild, files/embassy-mira-2.8.2-r2.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-mira/Manifest b/sci-biology/embassy-mira/Manifest index 8313029b6..a27a55b0d 100644 --- a/sci-biology/embassy-mira/Manifest +++ b/sci-biology/embassy-mira/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-mira-2.8.2-r2.patch 9423 RMD160 b9365ecedfc60214dd28e30ea18fe26c425ae011 SHA1 590e8e0c693a0323e9817bd4542f442a01047b63 SHA256 246850c658980eb99ace5525d0f1ebcefd78b1a4f0f40d7b1c44d14502b50f57 DIST embassy-mira-2.8.2.tar.gz 823636 RMD160 2df2b3102671bc74db93602d7c8ecaaf4f83435a SHA1 a87f51f1ad31d419b634a9e04e985a42f7cae4c2 SHA256 82a57cd526a4348a7456947e5ffc225fc42684bc21b5ec6996d99100f86d31ec -EBUILD embassy-mira-2.8.2-r2.ebuild 377 RMD160 ed50a51cc36d286adfb69c80240ad66d3a0977d0 SHA1 98fe62b9e2e650b7cf22d18e8aaab8fcfdae7b7f SHA256 ca7df07746c0120871cd3622384c257088c1ef5325b0d8cb8375e43dbdbe3de4 -MISC ChangeLog 1456 RMD160 1fc5bc800ea82e7422fa361221d93e80e9166859 SHA1 ba885827be8d691446989cdb5336d24d3e6c24fa SHA256 d47c1e2717426c48c3aea633325a675fd0fa7b91a01a673096aef516fc912e29 +EBUILD embassy-mira-2.8.2-r2.ebuild 372 RMD160 eb6f2b4c0e8cbb2e55af13abcf1e15937b87628f SHA1 685e20d4db697420a8b543e0447daabde5b5c8d1 SHA256 ba38a67f3fb106e571e65a0daf878034acc8daba7e51273f90a1230ac4995339 +MISC ChangeLog 1603 RMD160 0999a452469a08de19c034de11a26dd55116dbb1 SHA1 aee5f16ea3bacda045fc745dac963af12ccea19c SHA256 6c14bde979e50dcc293a643b1bfb6ee6d1ff8016c035fb8cc62091b7e136e1d2 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F9n0ACgkQgAnW8HDreRZb0gCgktn50/6fkfzIDoxuuZAfWTnj -6FQAn092q1Xz09WZ9R5S2MfQ8BY7JcOX -=NXPa +iEYEAREIAAYFAk4GAvAACgkQgAnW8HDreRbOPQCgpjSxLn/J5uk2m/FHLNBFosmX +79sAoLbRJN9H7GPg8Hr1S1ocfz9vWmRR +=ji/h -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-mira/embassy-mira-2.8.2-r2.ebuild b/sci-biology/embassy-mira/embassy-mira-2.8.2-r2.ebuild index 30fb46cb3..2ed8a9fe9 100644 --- a/sci-biology/embassy-mira/embassy-mira-2.8.2-r2.ebuild +++ b/sci-biology/embassy-mira/embassy-mira-2.8.2-r2.ebuild @@ -8,4 +8,4 @@ EBOV_DESCRIPTION="Fragment assembly add-on package" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-mse/ChangeLog b/sci-biology/embassy-mse/ChangeLog index 986307764..0d60fafd8 100644 --- a/sci-biology/embassy-mse/ChangeLog +++ b/sci-biology/embassy-mse/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/ChangeLog,v 1.35 2010/01/01 22:05:28 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-mse-3.0.0.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-mse-3.0.0.ebuild, files/embassy-mse-3.0.0.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-mse/Manifest b/sci-biology/embassy-mse/Manifest index ae991627e..c47861b82 100644 --- a/sci-biology/embassy-mse/Manifest +++ b/sci-biology/embassy-mse/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-mse-3.0.0.patch 10900 RMD160 171a943e032522e6de380e699c9a917c634d7fc7 SHA1 28d39621f0b0924bf4c5982a5b50376453d6410f SHA256 1d900f8fb9d6d45f160a33faeb41ba5dc10413c5034d0ee0dcb020a5414bb5ce DIST embassy-mse-3.0.0.tar.gz 435315 RMD160 9e94bdc1cbff5b684a6d7f33a7a95de33c1b910e SHA1 bae84ef0154f444037653df322fb605d013dca0c SHA256 f3bb205b197d4cc4ad7d6ee8e3696eb59d84a8b60a8369d4a645871d0c9619c3 -EBUILD embassy-mse-3.0.0.ebuild 547 RMD160 5949b0db7f8addc9dafca3b3f08b5eda51824e18 SHA1 da9045e9c1c5cf5a0d5e805613c2a0243cb99bc8 SHA256 236230400b07988f6a06de2c73e4913612fc6934339120a79d9fad1cf18ee4b9 -MISC ChangeLog 5598 RMD160 cd7c8a60b5413e0bbb0b12a2f80b8f70082ea099 SHA1 f4076a406c8e947ce68f53a751b5d3dede0da448 SHA256 b27312004ed0af85916da8c9708b3174da48f0a0055d23c493b533f423477932 +EBUILD embassy-mse-3.0.0.ebuild 542 RMD160 f519ac8277e5100da25dae0d36786977f67768f4 SHA1 78d82b15444c953b6ed3c75f612bf8a1dde3c82b SHA256 93bd99eecc5d4b1d9f8032067e664785217729bc107bbc6d37a80bfd421d0161 +MISC ChangeLog 5741 RMD160 a71180e4544aa4d85fbecedd927b905b0aeb9070 SHA1 90c869530f6fcec35ec1359d9b4894b1b1699aaa SHA256 8bd4a2e45a88ef282c2975ef1b8ba0f94ab9700127865e770d2c05ceda041f90 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F+L4ACgkQgAnW8HDreRYFjQCdHmwyYJP/PHR0fJ1l1YZvvsrh -gtEAn3p6LUF1syBnnokCmBkqPPU0HYiy -=BiI2 +iEYEAREIAAYFAk4GAwQACgkQgAnW8HDreRYgEACgyKU8ESvF1rlyKi0Gk4EdwgYW +yOUAn3i6RJmUPE/3Pzir3sgbn4zRsMn/ +=eGWh -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-mse/embassy-mse-3.0.0.ebuild b/sci-biology/embassy-mse/embassy-mse-3.0.0.ebuild index dd6a473f0..e8bf5541f 100644 --- a/sci-biology/embassy-mse/embassy-mse-3.0.0.ebuild +++ b/sci-biology/embassy-mse/embassy-mse-3.0.0.ebuild @@ -8,7 +8,7 @@ EBO_DESCRIPTION="MSE - Multiple Sequence Screen Editor" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" IUSE+=" ncurses" diff --git a/sci-biology/embassy-phylipnew/ChangeLog b/sci-biology/embassy-phylipnew/ChangeLog index 048d0bd1f..4053bf0b3 100644 --- a/sci-biology/embassy-phylipnew/ChangeLog +++ b/sci-biology/embassy-phylipnew/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylipnew/ChangeLog,v 1.12 2010/01/01 22:02:06 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-phylipnew-3.69.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-phylipnew-3.69.ebuild, files/embassy-phylipnew-3.69.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-phylipnew/Manifest b/sci-biology/embassy-phylipnew/Manifest index 12722791a..1dd10e35e 100644 --- a/sci-biology/embassy-phylipnew/Manifest +++ b/sci-biology/embassy-phylipnew/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-phylipnew-3.69.patch 9615 RMD160 3933c0479d9bee7b725c7783e652334c1d634d9b SHA1 a8ad42aea033cc3949972a7a5299e551617a9587 SHA256 8b918547f1916c4c8d9127a349714388cfe923c0fa5f65994011c44246bff4d0 DIST embassy-phylipnew-3.69.tar.gz 1667760 RMD160 8cb425f8e7af99d0081d2014403de74ad8e84feb SHA1 65e265190873b14c7449f6d53cc017ea90b612b6 SHA256 2e74ce4f70ad5421ea81e84c199a08bfb4a236e2cf2769be4f309c4badd1302b -EBUILD embassy-phylipnew-3.69.ebuild 390 RMD160 f234e4a08a8ee873f1fca5c2a71d8a685c04959c SHA1 673343e393d6eac17de1cad71184290030cf8b81 SHA256 4ed839a310d8d029858e67aab6aa23ba9d9f9a8756e6881011c834250ec209e8 -MISC ChangeLog 2376 RMD160 e25cdc29505bb478e7b20f76559a5674e481fee1 SHA1 9f73f185f2c2aabcd5208ab919bbdb8f2d51598e SHA256 befa96d493e676d006232875c710abccc88e7a55f958a5dea886e89cd81818f8 +EBUILD embassy-phylipnew-3.69.ebuild 385 RMD160 99fe0e4c52cf4c2aa52f54bace2e3a41b1ed2172 SHA1 85471ce1481cd41592b925833e87eb1055b7b018 SHA256 1c75892670b87492e53e6b3004cebefb21c4a2b52d5c0be0995755cb9ba29542 +MISC ChangeLog 2524 RMD160 45961c99f77705ac0af8d8833ba2f23c7d46feb2 SHA1 e50c3ba423e3675086d63056833150bdb1a44dba SHA256 888f40b1dc771f9e4d0bd7fae9da8e2a538454ca13ef011044f7c963d2e02bf9 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F+joACgkQgAnW8HDreRaRGgCfd3+F9IEe7f120C+q0EmPVY43 -hwAAoKzU7TnMVj8gw5X8XHYVayXX/xmD -=kuSG +iEYEAREIAAYFAk4GAyUACgkQgAnW8HDreRb+9wCeMWpXq2DOLHuGXsCEwLIHyEIV +8eUAoK4HYQ9U/KiJkhb06FIMRBh3cgmF +=ZZ/w -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.ebuild index 6767ae7bf..34691a5ef 100644 --- a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.ebuild +++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.ebuild @@ -10,4 +10,4 @@ inherit emboss LICENSE+=" freedist" -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-signature/ChangeLog b/sci-biology/embassy-signature/ChangeLog index b541cb909..9bfed99ea 100644 --- a/sci-biology/embassy-signature/ChangeLog +++ b/sci-biology/embassy-signature/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-signature/ChangeLog,v 1.19 2010/01/01 21:59:44 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> + embassy-signature-0.1.0-r5.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-signature-0.1.0-r5.ebuild, files/embassy-signature-0.1.0-r5.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-signature/Manifest b/sci-biology/embassy-signature/Manifest index aee7759ba..1cbf4bde6 100644 --- a/sci-biology/embassy-signature/Manifest +++ b/sci-biology/embassy-signature/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-signature-0.1.0-r5.patch 9515 RMD160 d49cc11f72e7538feeb2326846a30cc902c789d8 SHA1 a208e5469d61c77a10b2e729e729782ba08cd97b SHA256 2a6d31d71cc2b3206e88fd21ff69714d2fa97695285f69a6033c9416eb7da4cf DIST embassy-signature-0.1.0.tar.gz 571008 RMD160 d69cbdeb8461d4f5596546dad9d1b7afc14df672 SHA1 bd9834fe0aeb7b6f6fd1a46550adc6be06d74566 SHA256 feaec1c3d3a8a2b98bb691137aa5ac099f7cef6579150fdb1429fcfc5db01024 -EBUILD embassy-signature-0.1.0-r5.ebuild 373 RMD160 239bf7f85b665e3e673768af1a93241e2786ec5c SHA1 3b23acc995d315a71192ec99512112a4f6067759 SHA256 14410def1ecf2e1c48dfaf0fd7124f9af64555c62f216a8e551e7eda67e8084f -MISC ChangeLog 3461 RMD160 ac4a7335f4d3e829ae7a0873dc6ceb191c53bfbc SHA1 f7066903c1ff313981f088665d7c602df5848f9a SHA256 e5ee2628e7fc82f59374369d9eb72090f555e6181345456d5e6cb6dbd13beb1c +EBUILD embassy-signature-0.1.0-r5.ebuild 368 RMD160 d189d471bf91102c82e851c88d7958258513fe9d SHA1 4f9cb575a53614c50eb02f2b5f6e31d09562010a SHA256 9bb72ba36fa13d2bdd427afbcc875f399f93f498c13da7209fe6cea3bf2235c4 +MISC ChangeLog 3615 RMD160 a7579b01318721b2d095af930f710436562bc49f SHA1 4fc57225fca7d622545a6851c844dd4989adc22c SHA256 be033c1257bb9284fd768df472301b9ffa51983c36ea9f8ab48aa3970bd4db78 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F+8oACgkQgAnW8HDreRbvSwCfXEik12rFDZ7o2XrbWi/44jCA -eMIAn0sBel1PQpltnAH+iwwgh+uZx0VD -=Ec7L +iEYEAREIAAYFAk4GA18ACgkQgAnW8HDreRZggACgrFL9oLCRLQplQkq7dZiG16oS +XekAoI9u0kMvGam+ETBTM/StG0qhj9ly +=NIgo -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-signature/embassy-signature-0.1.0-r5.ebuild b/sci-biology/embassy-signature/embassy-signature-0.1.0-r5.ebuild index de1c6abcf..77aefb434 100644 --- a/sci-biology/embassy-signature/embassy-signature-0.1.0-r5.ebuild +++ b/sci-biology/embassy-signature/embassy-signature-0.1.0-r5.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="Protein signature add-on package" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-structure/ChangeLog b/sci-biology/embassy-structure/ChangeLog index 4fe54066c..7afd64dc4 100644 --- a/sci-biology/embassy-structure/ChangeLog +++ b/sci-biology/embassy-structure/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-structure/ChangeLog,v 1.19 2010/01/01 21:57:51 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> + embassy-structure-0.1.0-r5.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-structure-0.1.0-r5.ebuild, files/embassy-structure-0.1.0-r5.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-structure/Manifest b/sci-biology/embassy-structure/Manifest index db9211988..4da8e216c 100644 --- a/sci-biology/embassy-structure/Manifest +++ b/sci-biology/embassy-structure/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-structure-0.1.0-r5.patch 9522 RMD160 e89d1f49221585e6e25f60aa625ca50727c61da4 SHA1 bf3cc5df2e00f76acfd38fdb555330022b87098f SHA256 106dec75227d9708ec61c0ef9ed5d453e0b1b22dbe3df8443f1c3c27961a6a88 DIST embassy-structure-0.1.0.tar.gz 531604 RMD160 33d351f0b107637d59c1623a9cbd6e97e1f3f17a SHA1 ec19fd6c69e7ed3be894c588fecdd77b98bcb0b8 SHA256 df2dc789544e61f695438e3117921ecef78739963169672e80c3394659720afa -EBUILD embassy-structure-0.1.0-r5.ebuild 373 RMD160 739d25d4a3e8cda97ace59a335a03e72e426b50f SHA1 dfe56ad9090bde5cac1cb06ebfd011236c631845 SHA256 7823fb3b96a2cbf4d55a7061a13e07c187a941640d155ba36d19012e02d3b264 -MISC ChangeLog 3461 RMD160 8515547b3d7b6a2c69387a7f85ecd7120b3911ed SHA1 5057daf1ba8c69a89a55d1d8eb9863373f0d7052 SHA256 2317c7e53ff660fcc4edaf3e8813c9a61e97cf1d952d8fd87492175fdb9396e9 +EBUILD embassy-structure-0.1.0-r5.ebuild 368 RMD160 82400a4204df48c7626351eb58e4f7fd649d123e SHA1 31d3ea026687f378534138b5bd2937671d5a9a1f SHA256 8a8f9eea06d4c795ee65be4bf19224bbdf05dcff6a9410dea2e614d7649f9c3a +MISC ChangeLog 3615 RMD160 20a720b90a2f6f12cb1c2adc90427d06bfe3c8cc SHA1 ee8c349ec0dce53279316fe40511097f2fedcd92 SHA256 99fe3e9e66b374ae2916a5ea372caedaba92bf698efa217eec78d78b577e37ee MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F/DIACgkQgAnW8HDreRYFpACfciQyXDUM2jBuWVCNX+J8vcSz -cjsAoMFM5gfZF/jx7dJBxqHA9weRfqa4 -=6ipH +iEYEAREIAAYFAk4GA3oACgkQgAnW8HDreRZnyQCfTSTEatJJCkBw8KhZVkeQfbAm +AjsAoLlJFz161oJYtulYWE3yqZfhb6Ql +=Z80J -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-structure/embassy-structure-0.1.0-r5.ebuild b/sci-biology/embassy-structure/embassy-structure-0.1.0-r5.ebuild index 4af39271b..ac6658955 100644 --- a/sci-biology/embassy-structure/embassy-structure-0.1.0-r5.ebuild +++ b/sci-biology/embassy-structure/embassy-structure-0.1.0-r5.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="Protein structure add-on package" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-topo/ChangeLog b/sci-biology/embassy-topo/ChangeLog index bc25e4ebd..5ad2bc721 100644 --- a/sci-biology/embassy-topo/ChangeLog +++ b/sci-biology/embassy-topo/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-topo/ChangeLog,v 1.29 2010/01/01 21:54:52 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-topo-2.0.0.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-topo-2.0.0.ebuild, files/embassy-topo-2.0.0.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-topo/Manifest b/sci-biology/embassy-topo/Manifest index cd50c3164..6bce89048 100644 --- a/sci-biology/embassy-topo/Manifest +++ b/sci-biology/embassy-topo/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-topo-2.0.0.patch 9416 RMD160 fdaed3604e8a8d041a189291067332358ed9d349 SHA1 26768d5f14221a40e315b2ed99bc2cd73bc219b2 SHA256 d6c7b9bfd31487b14a608f758e38698a2ace3cad57b8c321fd8d69c1f5d75672 DIST embassy-topo-2.0.0.tar.gz 386287 RMD160 d25cdde9ea76253c088754f1633389ce87e79866 SHA1 c6373211ed36866497ad54a6f8bf9bc0aa4733bc SHA256 023e1f1e92e0372c4029c9e19043af0416d0e294440bb368d30126c5ed330691 -EBUILD embassy-topo-2.0.0.ebuild 373 RMD160 6c3eb53aa44a640807cf562541a574749223da63 SHA1 737062a13b260b7cf1123526aad06112e7f4d20f SHA256 654f9f4ff5929f2ab6f94b1a3fd7c3f6fea696a80be610fccb84e78f8fa73d79 -MISC ChangeLog 4778 RMD160 dc4832b8a5a100c6034a1dc8e6e9b821334a7524 SHA1 d3301ecf66f677a5dd408e61c43135172da5f8df SHA256 8ac4f880d19be2a42e48325c3994391a7cab3a84d231b9a8a0d5976469b3245f +EBUILD embassy-topo-2.0.0.ebuild 368 RMD160 26cc07ab59586b39677492099bc8a5765eb2ade0 SHA1 c6ca98799deb4db707234a2bed49762bc0186ebd SHA256 4d4ab09f8f138533669553a1890a0bbcc025f2c1d3c58e6bb3785997c2b30ecd +MISC ChangeLog 4922 RMD160 8eb2223000309a5e863c613fe4604fcf26870aa3 SHA1 679e45de2387f0abe20536da5e4f94228cb09b21 SHA256 f2baeba6ee08d2dd039329c196b6f64ca4c3ece5b06e175b02aa128ed7533698 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F/PsACgkQgAnW8HDreRZDhgCfSaIUXc8dw4Funmc3tlTtlHZ5 -LiMAoKeN9DAY7CRN1N06tGiYXXwtDO6D -=XtB0 +iEYEAREIAAYFAk4GA5MACgkQgAnW8HDreRZcUQCfXEESoX45eJJV0tbSXobJvHPc +hcIAnAtw8YGpdrVOOVpzHpl7iMf6p6Ec +=2kVI -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-topo/embassy-topo-2.0.0.ebuild b/sci-biology/embassy-topo/embassy-topo-2.0.0.ebuild index 3090d47a6..02244e6f4 100644 --- a/sci-biology/embassy-topo/embassy-topo-2.0.0.ebuild +++ b/sci-biology/embassy-topo/embassy-topo-2.0.0.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="Transmembrane protein display" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-vienna/ChangeLog b/sci-biology/embassy-vienna/ChangeLog index 7df53c061..3d15b99f9 100644 --- a/sci-biology/embassy-vienna/ChangeLog +++ b/sci-biology/embassy-vienna/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-vienna/ChangeLog,v 1.8 2010/01/15 22:47:16 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-vienna-1.7.2-r2.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-vienna-1.7.2-r2.ebuild, files/embassy-vienna-1.7.2-r2.patch: Fixed for reviewed eclass diff --git a/sci-biology/embassy-vienna/Manifest b/sci-biology/embassy-vienna/Manifest index 1d018c5d5..066106a0a 100644 --- a/sci-biology/embassy-vienna/Manifest +++ b/sci-biology/embassy-vienna/Manifest @@ -1,15 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX embassy-vienna-1.7.2-r2.patch 9731 RMD160 5cda4d8a04c252051a8affb85706648de8fa91a5 SHA1 e7a6d11b6ab4c8f353a530c42d6c677457e15389 SHA256 c5de170aaf19f0339780120132f97a5f26a48b26d739a5bdb772fdb6d26e3bce DIST embassy-vienna-1.7.2.tar.gz 652433 RMD160 753b37bfaa8f362ebc46fb96955537fd82c627c4 SHA1 4eb8f80c9579a96b198c35ec3dba4b93821789f8 SHA256 61c60e4335a716cbc80e6fab47268de64c6c377c0a052686cd98822cf7270d7c -EBUILD embassy-vienna-1.7.2-r2.ebuild 380 RMD160 9105a9723b81e1dce6ccfde70784b4e31970795e SHA1 b44cb11627eca23df2ddcaa922f03f3ff0913808 SHA256 0d56b3ca1f4015a0649eccc94e8ca3ba12a7000036156d537e0ec8a24794bea1 -MISC ChangeLog 1873 RMD160 3633f62b4770438afc5afe6f3171f2f05778bbbb SHA1 a3cd44496536a20d1138c4bd80edaa11605fb48a SHA256 c3ff48d00893aac7fa9fd323eaf58a8a86d8379db26aef358151bf5212fdbce2 +EBUILD embassy-vienna-1.7.2-r2.ebuild 375 RMD160 ce51a1e63695d6286034c08d3cbf2a8d02f61b2f SHA1 3052730952a478de52507eb3dd327a8b0fd9d710 SHA256 fbe5d6d1d1743f1a35f249856e07058d3188dec495ce225479888c202f547b8f +MISC ChangeLog 2022 RMD160 98a74e8684854f45e144475f5ff89d4e443f72be SHA1 e858b3aff5806edfec90760e7e8dea8f24e28b21 SHA256 f7dbc9853c89e650518217552092bad9aa20c27ab8e343db50ebde31bb1c85fa MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2F/poACgkQgAnW8HDreRYkigCeJpDVnreI/Rv26tHmb9NbhXq8 -AtkAnR5NrTa5En7RKtyNQK+QIM9hWbRj -=gOG8 +iEYEAREIAAYFAk4GA6QACgkQgAnW8HDreRa+ZwCcC+aDA2QRFokUmI+h52ofAMCe +WegAn1aNcFddrtJ2wh1SJVoZ7UKqdBBx +=iToN -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2-r2.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2-r2.ebuild index 9a7b8e53c..594278f81 100644 --- a/sci-biology/embassy-vienna/embassy-vienna-1.7.2-r2.ebuild +++ b/sci-biology/embassy-vienna/embassy-vienna-1.7.2-r2.ebuild @@ -8,4 +8,4 @@ EBO_DESCRIPTION="Vienna RNA package - RNA folding" inherit emboss -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy/ChangeLog b/sci-biology/embassy/ChangeLog index a08d9efbe..445246a8e 100644 --- a/sci-biology/embassy/ChangeLog +++ b/sci-biology/embassy/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy/ChangeLog,v 1.33 2010/01/01 21:35:29 fauli Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-6.3.1.ebuild: + Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 + 21 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-6.3.1.ebuild: Fixed for reviewed eclass diff --git a/sci-biology/embassy/Manifest b/sci-biology/embassy/Manifest index 0ee4f05b5..6432e5073 100644 --- a/sci-biology/embassy/Manifest +++ b/sci-biology/embassy/Manifest @@ -1,13 +1,13 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 -EBUILD embassy-6.3.1.ebuild 1104 RMD160 e1332acc8a61e2be31c5bf1957caa983b63e011c SHA1 ba3effa2b9c800f9d29d001e6c4c537f4eae2b7b SHA256 d7a587d1110d29faa63903106edf31faa067dc075d38de5fccb2664207f56dd6 -MISC ChangeLog 5213 RMD160 77f058ea7c5e40d5e101eeaae41e1c93f3b96f4e SHA1 82af9df083283693de75a856497f4bdbce85aba1 SHA256 1fdaa89b82ca06e9c892c9e003f565e4d1a5cd8f4fdf8ecc2a5392e20c2ac834 +EBUILD embassy-6.3.1.ebuild 1099 RMD160 dba540412b7ce2f9b0266facfc37e4ef95e28b58 SHA1 efabf268999265a10e37a7103887bd376c181a7d SHA256 4e30ae47578b0016d495816bb6ebb83bdd8e388b291feaa621214b1580cd8135 +MISC ChangeLog 5352 RMD160 3630f8fee437d95096271e1add960c3ae900b9a1 SHA1 861164d561f325c35e0b0db79892780e1eda3a80 SHA256 6afc7b4a2b9be3b73c648b5e1a2d00c604a39efd3813df7c4a2c0a1ec0f3eae3 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2HQLUACgkQgAnW8HDreRb48ACeNzOEItkFGpd2DSSlkqjUw8iq -FLEAnRD2A6r4lrH0ikbZFJTkrIr1jcPx -=0Chi +iEYEAREIAAYFAk4GAZgACgkQgAnW8HDreRbDwACfVEAGTczIYp6yJQ1dVJKxsdpg +wZMAoJicRtMe/NclSS+wz5SLObdgUjH1 +=S7it -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy/embassy-6.3.1.ebuild b/sci-biology/embassy/embassy-6.3.1.ebuild index 0cceb185c..38ad021a2 100644 --- a/sci-biology/embassy/embassy-6.3.1.ebuild +++ b/sci-biology/embassy/embassy-6.3.1.ebuild @@ -10,7 +10,7 @@ DESCRIPTION="A meta-package for installing all EMBASSY packages (EMBOSS add-ons) SRC_URI="" LICENSE+=" freedist" -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" RDEPEND+=" =sci-biology/embassy-cbstools-1.0.0-r2 diff --git a/sci-biology/est2uni/Manifest b/sci-biology/est2uni/Manifest index 29191fd2c..211a599bd 100644 --- a/sci-biology/est2uni/Manifest +++ b/sci-biology/est2uni/Manifest @@ -1,5 +1,6 @@ -AUX 9999-est_clustering.pm.patch 1276 RMD160 4a54b28c9a67ae8476255a4063768a1c7b466357 SHA1 1d255394dad2f608bd91f6064232a3cd431e368d SHA256 c289866a862a18a9385db9931c3c0c9175334e829819f075cc7fbf7e8bbd83ce -AUX 9999-pipe_db.pm.patch 534 RMD160 8b2a5ef4de3a2c65eb65476cbb4decdad3eb8a74 SHA1 46509d05f01ae53764b4947ddb663edbb3bfee9d SHA256 11aa489e406bceabdd3b7d532fbca69ede1c0a116cc7a38ae9ea32dafc41f54c +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX 99est2uni 82 RMD160 4171612511e63f41fa57aa743a435e4e5ca811d1 SHA1 a51b17f763855cda65e3bf5f401dccab231e1593 SHA256 4317ba1309d2506682d5146f7fb52f388b368bfd2ab33b4a2cf95ec8b117341e AUX est2uni 82 RMD160 4171612511e63f41fa57aa743a435e4e5ca811d1 SHA1 a51b17f763855cda65e3bf5f401dccab231e1593 SHA256 4317ba1309d2506682d5146f7fb52f388b368bfd2ab33b4a2cf95ec8b117341e AUX est_annot.pm.patch 19656 RMD160 83c75544edf45b7dffe92b97ec1935ec4774241d SHA1 f6051670594093ba89cb259cb0427222bf4a3f02 SHA256 fdfb19e711a05b02016ffbe57f5d68f5d7b8746690445aafa2cab6ebf8ddd058 @@ -16,9 +17,14 @@ AUX tgicl_files.patch 865 RMD160 cc782fcdf0ae723b69e2b9d7135ad7236a960dc7 SHA1 0 DIST GO.terms_and_ids 1773108 RMD160 6df24848cedea76de66bbebf7eaa5eadd58e016c SHA1 e73465e4c1606245be723417adf9bcdc5c454965 SHA256 8a6d670f4ecdfa81a609abdd959d13fb9f695132eb08a2b412a8d80b50fd7e64 DIST UniVec 1062966 RMD160 ef634cd9e8996d8e3dc6e5fdbabb09ee4f5df2c3 SHA1 c599178ef9e6c6865fd531018145ed43851e5e01 SHA256 6fc0e3644a2ecb59705801416d76d7d74aa8fa5788e955a024b2d9614376f425 DIST UniVec_Core 542650 RMD160 a8cf42b9015622a8ac52839c7b794bbad4c1f92a SHA1 6ebaa99115661302125bd5b15a7caace264f2cda SHA256 7456353d072da508538052286c82ff5fec740a6ceac5621f68fd4eb35bdff9ef -DIST est2uni.tar.gz 10251279 RMD160 a208295065d68e4d68804b0b5c840f877111c0d6 SHA1 f10adac451f739f0ef97aea153eb4ea2066c8229 SHA256 347f668d8a18bedafe8644fe2bcd7d184dd77f1c98aabfbfab70767ceb819874 DIST est2uni_0.27.tar.gz 4616613 RMD160 06ec260f79fe11f7779b75aad825e665f421d4eb SHA1 5ee9b5dc51f4829c5ed0d4ddd47bb68e7f3c43ee SHA256 33d2f2981ca70fa6707d3a2f310c0492cd12a430b6bb9b7ad8697a8fc3305cd4 DIST gene_ontology.obo 19990996 RMD160 b3584271ab0a05909cde9a92e6eb635b08fe23be SHA1 bdb9d396d4320bf639be310cf6f93b08b25ef0e9 SHA256 7f70c7a1dd4b75f6055f05c5e5445a49ecf20fed8172d54ec2d04722842ff19b -EBUILD est2uni-0.27.ebuild 3258 RMD160 4cb0a29cfaaef9573f4e35dbcc649233b7f15563 SHA1 1b9d7ef1df4164e48f7d1dc0fce6367e29049f68 SHA256 0e9fb1acb658babb5de052910db4f86ae1dcd7108ca6aa11a03d150ad0f90838 -EBUILD est2uni-9999.ebuild 3351 RMD160 2a5eb12cb460e76c2bdea8f011e40b67e4a1a62a SHA1 8a422f75cf307669056b947a70126b8bacd9e46c SHA256 9816a7d559440e3cee5dd1e6c8cd423be330f32c9aa700d1d674d1d303277ad6 +EBUILD est2uni-0.27.ebuild 3292 RMD160 d676915e49ef8f3ec04da0391945441fd47028f1 SHA1 a349fbd92f6ec096f5cad8dbabb2769594531111 SHA256 e47c997ced2b2b01e4abc509349e389e9f1e3b272e696c606aa9d010984f2821 MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EiSQACgkQgAnW8HDreRaZuwCfYMccT5NROdxtN7jg0sFQZ4vh +QE4AoLcFDH3moqCaBR2DMkuxrBu4i9NL +=ZlWM +-----END PGP SIGNATURE----- diff --git a/sci-biology/est2uni/est2uni-0.27.ebuild b/sci-biology/est2uni/est2uni-0.27.ebuild index 45eaf4290..7252b2f8a 100644 --- a/sci-biology/est2uni/est2uni-0.27.ebuild +++ b/sci-biology/est2uni/est2uni-0.27.ebuild @@ -4,16 +4,18 @@ EAPI=3 -inherit webapp eutils perl-module +inherit eutils perl-module webapp DESCRIPTION="EST assembly+annotation: a perl-based analysis pipeline including php-based web interface" HOMEPAGE="http://cichlid.umd.edu/est2uni/download.php" -SRC_URI="http://cichlid.umd.edu/est2uni/est2uni_0.27.tar.gz - ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec - ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec_Core - http://www.geneontology.org/ontology/gene_ontology.obo - http://www.geneontology.org/doc/GO.terms_and_ids" - +SRC_URI=" + http://cichlid.umd.edu/est2uni/est2uni_0.27.tar.gz + ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec + ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec_Core + http://www.geneontology.org/ontology/gene_ontology.obo + http://www.geneontology.org/doc/GO.terms_and_ids" + +SLOT="0" LICENSE="GPL-3" KEYWORDS="~amd64 ~x86" IUSE="" @@ -31,10 +33,10 @@ RDEPEND="${DEPEND} sci-biology/ncbi-tools sci-biology/bioperl sci-biology/exonerate - perl-gcpan/go-perl www-servers/apache >=dev-db/mysql-4.1 <dev-lang/php-5.3" +# perl-gcpan/go-perl S="${WORKDIR}"/est2uni @@ -45,7 +47,7 @@ src_prepare(){ } src_compile(){ - "$(tc-getCC)" external_software/sputnik/sputnik.c -o external_software/sputnik/sputnik + $(tc-getCC) ${CFLAGS} ${LDFLAGS} external_software/sputnik/sputnik.c -o external_software/sputnik/sputnik || die } src_install(){ diff --git a/sci-biology/estscan/ChangeLog b/sci-biology/estscan/ChangeLog new file mode 100644 index 000000000..ff0f2e4b0 --- /dev/null +++ b/sci-biology/estscan/ChangeLog @@ -0,0 +1,12 @@ +# ChangeLog for sci-biology/estscan +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 23 Jun 2011; Justin Lecher <jlec@gentoo.org> estscan-3.0.3.ebuild, + metadata.xml: + Streamlined fortran-2 eclass usage + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> estscan-3.0.3.ebuild, + metadata.xml: + Added fortran-2.eclass support + diff --git a/sci-biology/estscan/Manifest b/sci-biology/estscan/Manifest index 843cd8426..e41936f81 100644 --- a/sci-biology/estscan/Manifest +++ b/sci-biology/estscan/Manifest @@ -1,3 +1,6 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST At.smat.gz 32314 RMD160 5c66e467d20e1ce43dce35cf20540649bbcf2879 SHA1 bd3e2d87be468e7d9c46557bce68e94bdd3f1aa2 SHA256 7f41329858b19ea13809becf58c7262b48dd8070dc38894b8ad7c55adcdd4c2a DIST BTLib-0.19.tar.gz 36283 RMD160 14ae4a24c81a381e9a75ddcde7552a1f9dc301b8 SHA1 7a0545cb64976ee61e76a80a9ee1a87eb1747078 SHA256 0acd6446031222b8fd5bd11eb3ec6c3164bc50491feef765c052689d9c3ee302 DIST Dm.smat.gz 31711 RMD160 1e77b7f743ea9198108dff3dec2e8fd64ba8751c SHA1 6dd589a2dac0d4ea51ad085a835a5100b5eab8e1 SHA256 1f741836aa2b4ed96ab9ea6adb883eaa4d8d95610bd7a1ac484193ab30afca1d @@ -7,5 +10,13 @@ DIST Mm.smat.gz 62711 RMD160 30cf8dd0d944afcae7dd05b30bc08820e303c7c4 SHA1 2d0d5 DIST Rn.smat.gz 32388 RMD160 4ff99c8502aa914c85aeaf19f98bc7362ab70cb0 SHA1 060e66141a19302e805323322ab219d990cf4592 SHA256 2e0a9b3347a8d216a026f98e38243d207e683bc50ac5be35c4c24f5ee1803cb8 DIST estscan-3.0.3.tar.gz 46412 RMD160 dc5e12e8196837585c405163f643e2da0c84bd79 SHA1 8af2128aaa02c50d1d3cfa75188fac038381975c SHA256 037dc8770681ed12406a789ea292462a4ce5d89b0e906a1a3340aa4debc71e2f DIST user_guide_fev_07.pdf 327005 RMD160 99f838a2c61c82a5078fb49e06ab8c8a7a8c1509 SHA1 335b3bacf0af8947db57324a702d335e72d58abd SHA256 416998f9fc282a53679fd56585b468ccebc4463e61ee5e989d9b426ed6f725fd -EBUILD estscan-3.0.3.ebuild 3959 RMD160 1e0db12b467d3d7cece9b5c3247214c702d783ce SHA1 aac4d9d5d39a9b239bf1d3b16567b9aa2469f5c5 SHA256 14e60176ea0493ec0e28ebca0e8b7165363b70e1165357c29ea6a49d804cb886 -MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +EBUILD estscan-3.0.3.ebuild 3627 RMD160 04e489ba6db85e382a3d55adbab168e46f09e791 SHA1 3412b7e3aa90ee4392a48b59fc3cd5712f0c3a1e SHA256 64c25c435fdaa15c814707ed13d3ad42ca7cac6f5cbb29d1d52ff432359aa4cc +MISC ChangeLog 362 RMD160 fd6d014788fd1c68fd8e1e58b37c2ac0585fdb4d SHA1 5079e398e369900824f8b7f4d3ed176df88a1fd2 SHA256 96f00043d927fffa618ad23bc67589ce75caff6294afd1f4e16795cb47b09082 +MISC metadata.xml 326 RMD160 cdc20d05766f861cff6889339611ca1c22579631 SHA1 dddeeb441b46d5437d1883f7c44ea26ad704344e SHA256 530e03907f86440fdc52832f744b709dde2ee85492cad7b8a263544a93ea0bea +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4DAxcACgkQgAnW8HDreRYbrQCfRdlKYlwAQQu22Y741J7tR7t6 +jp0AoIpbBVtLAlueTxY2BLymUs2wbbGz +=zCkB +-----END PGP SIGNATURE----- diff --git a/sci-biology/estscan/estscan-3.0.3.ebuild b/sci-biology/estscan/estscan-3.0.3.ebuild index ed573427a..d2828605a 100644 --- a/sci-biology/estscan/estscan-3.0.3.ebuild +++ b/sci-biology/estscan/estscan-3.0.3.ebuild @@ -1,49 +1,54 @@ -# Copyright 1999-2008 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=4 -inherit eutils toolchain-funcs perl-module +inherit eutils fortran-2 perl-module toolchain-funcs -DESCRIPTION="Predict coding regions in DNA/RNA sequences even in low-quality reads with frameshift-causing errors (supersedes ESTscan and ESTscan2)" +DESCRIPTION="Prediction of coding regions in DNA/RNA sequences" HOMEPAGE="http://sourceforge.net/projects/estscan/" -SRC_URI="http://downloads.sourceforge.net/estscan/estscan-3.0.3.tar.gz - http://downloads.sourceforge.net/estscan/At.smat.gz - http://downloads.sourceforge.net/estscan/Dm.smat.gz - http://downloads.sourceforge.net/estscan/Dr.smat.gz - http://downloads.sourceforge.net/estscan/Hs.smat.gz - http://downloads.sourceforge.net/estscan/Mm.smat.gz - http://downloads.sourceforge.net/estscan/Rn.smat.gz - http://downloads.sourceforge.net/estscan/user_guide_fev_07.pdf - http://downloads.sourceforge.net/estscan/BTLib-0.19.tar.gz" +SRC_URI=" + http://downloads.sourceforge.net/estscan/estscan-3.0.3.tar.gz + http://downloads.sourceforge.net/estscan/At.smat.gz + http://downloads.sourceforge.net/estscan/Dm.smat.gz + http://downloads.sourceforge.net/estscan/Dr.smat.gz + http://downloads.sourceforge.net/estscan/Hs.smat.gz + http://downloads.sourceforge.net/estscan/Mm.smat.gz + http://downloads.sourceforge.net/estscan/Rn.smat.gz + http://downloads.sourceforge.net/estscan/user_guide_fev_07.pdf + http://downloads.sourceforge.net/estscan/BTLib-0.19.tar.gz" -LICENSE="estscan" SLOT="0" +LICENSE="estscan" KEYWORDS="~x86 ~amd64" -IUSE="icc ifc" +IUSE="intel" -DEPEND="icc? ( dev-lang/icc ) - ifc? ( dev-lang/ifc )" - -RDEPEND="" +DEPEND=" + virtual/fortran + intel? ( + dev-lang/icc + dev-lang/ifc )" +RDEPEND="${DEPEND}" S="${WORKDIR}" -src_compile() { - # - sed -e 's/\\rm -f/rm -rf/' \ - -e 's/^ LDFLAGS = -lm/LDFLAGS = -lm/' -i "${P}"/Makefile || die "failed to edit Makefile" +src_prepare() { + sed \ + -e 's/\\rm -f/rm -rf/' \ + -e 's/^ LDFLAGS = -lm/LDFLAGS = -lm/' \ + -i "${P}"/Makefile || die "failed to edit Makefile" # fix hard-coded paths sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/estscan.c || die sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/estscan.spec || die if ! use icc; then - sed -e 's/^ CFLAGS = -O2/#CFLAGS = ${CFLAGS}/' \ + sed \ + -e 's/^ CFLAGS = -O2/#CFLAGS = ${CFLAGS}/' \ -e 's/^ FFLAGS = -O2/#FFLAGS = ${FFLAGS}/' \ -e "s/^ F77 = g77/F77 = $(tc-getF77)/" -i "${P}"/Makefile \ - || die "blah" + || die else # FIXME: I would use $(tc-getCC) instead of hard-coded icc but it gives # me gcc instead, same for $(tc-getF77) @@ -54,49 +59,55 @@ src_compile() { # FIXME: below as a dirty hack I force gfortran instead of ifort for # my testing purposes. Didn't ebuild contain "PROVIDES" line? # Same for FFLAGS. - sed -e "s:^# CC = icc:CC = icc:" \ - -e "s:^# CFLAGS = -O3 -ipo -axP:#CFLAGS = -O3 -ipo -axP:" \ + sed \ + -e "s:^# CC = icc:CC = icc:" \ + -e "s:^# CFLAGS = -O3 -ipo -axP:#CFLAGS = -O3 -ipo -axP:" \ -e "s:^# FFLAGS = -O3 -ipo -axP:#FFLAGS = -O3 -ipo -axP:" \ -e "s/^ CFLAGS = -O2/#CFLAGS = -O2/" \ -e "s/^# F77 = ifort/F77 = gfortran/" \ -e "s/^ FFLAGS = -O2/#FFLAGS = -O2/" \ -e "s/^ CC = gcc/# CC = gcc/" \ - -e "s/^ F77 = g77/# F77 = g77/" -i "${P}"/Makefile || die "sed failed to fix CFLAGS, FFLAGS, CC, F77" + -e "s/^ F77 = g77/# F77 = g77/" \ + -i "${P}"/Makefile || die "sed failed to fix CFLAGS, FFLAGS, CC, F77" fi - cd "${P}" || die "chdir "${P}" failed" - emake || die "emake failed" +} + +src_compile() { + emake -C ${P} - cd ../BTLib-0.19 || die "cd ../BTLib-0.19 failed" + cd ../BTLib-0.19 perl Makefile.PL || die "perl Makefile.PL failed" } src_install() { # FIXME: Some kind of documentation is in {P}/estscan.spec - cd "${P}" - dobin build_model estscan evaluate_model extract_EST extract_UG_EST extract_mRNA makesmat maskred prepare_data winsegshuffle || die "dobin failed" + cd ${P} + dobin \ + build_model estscan evaluate_model extract_EST extract_UG_EST \ + extract_mRNA makesmat maskred prepare_data winsegshuffle # the file build_model_utils.pl should go into some PERL site-packages dir # see {P}/estscan.spec # install the doc (but is not in ${WORKDIR} because src_UNPACK() failed on it - cd "${WORKDIR}" || die + cd "${WORKDIR}" insinto /usr/share/doc/ESTscan # grab the file directly from ../distdir/ - doins ../distdir/user_guide_fev_07.pdf || die "failed to install user_guide_fev_07.pdf" + doins ../distdir/user_guide_fev_07.pdf # install the default precomputed matrices - cd "${WORKDIR}" || die + cd "${WORKDIR}" insinto /usr/share/ESTscan - doins *.smat || die "Failed to install matrices" + doins *.smat # install BTlib (in perl) cd BTLib-0.19 || die - dobin fetch indexer netfetch || die "dobin failed" + dobin fetch indexer netfetch insinto /usr/share/ESTscan/ - doins fetch.conf || die "Failed to install fetch.conf" + doins fetch.conf # FIXME: install the *.pm files from BTLib-0.19 myinst="DESTDIR=${D}" - perl-module_src_install || die "perl-module_src_install failed" + perl-module_src_install einfo "Please edit /usr/share/ESTscan/fetch.conf to fit your local database layout." einfo "Also create your own scoring matrices and place them into /usr/share/ESTscan/." diff --git a/sci-biology/estscan/metadata.xml b/sci-biology/estscan/metadata.xml index 07b525505..a68ccd86c 100644 --- a/sci-biology/estscan/metadata.xml +++ b/sci-biology/estscan/metadata.xml @@ -6,4 +6,5 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> +<use><flag name='intel'> Use intel compiler</flag></use> </pkgmetadata> diff --git a/sci-biology/gap2caf/Manifest b/sci-biology/gap2caf/Manifest index 20729601e..124d0831e 100644 --- a/sci-biology/gap2caf/Manifest +++ b/sci-biology/gap2caf/Manifest @@ -1,4 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST gap2caf-2.1.0.tar.gz 92905 RMD160 8b19963ca9e845d9bae2e7fb8253cb77bae78857 SHA1 fdbffcd159caf75d95207e54cab3c8b8270cc8e8 SHA256 1fd237cf1e83c3c4c3b67d2d35c9f059cc7eda9f6ac7886fab994e2386283b9a DIST staden-2.0.0b8.tar.gz 4312143 RMD160 68b91a80fae29e0bf8f7e6ca1c0781591113684c SHA1 742092ff7bfb5acd3376ac85d5ab50507d1dd02f SHA256 c13aa0c22dcac6b10d13501dcb630efad51d7c171968e0bb30113667b49cfa9d -EBUILD gap2caf-2.1.0.ebuild 2821 RMD160 adbdb532f4294ffe925b3aa11a56d0d0665d24c6 SHA1 63295defe7ff7529e7227e06177bc11045399d91 SHA256 e1ed6dd95796da36e4dca7c6128646685fca722093f7125ca4ebcbf7746ef27d +EBUILD gap2caf-2.1.0.ebuild 2821 RMD160 ed85b15b7b8ed22673cedc4cd152e7ee1f849a37 SHA1 3f4f14dc652a405f84c505f60257328dd7a93c5b SHA256 0879da8f69fc4f0b5edcd0f8d8f34541f91dc47f824e2963e40a553fb6f17e53 MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EiSkACgkQgAnW8HDreRZ76wCeJr8TpFUJ0uDHlsOp7OWTId7f +qDoAnRKBm+3GzKuz/fgyA2iDPVwcKS2K +=7T4s +-----END PGP SIGNATURE----- diff --git a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild index 5aae263fd..861bbc8f0 100644 --- a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild +++ b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild @@ -4,7 +4,7 @@ EAPI=3 -inherit eutils autotools +inherit autotools eutils DESCRIPTION="GAP4 file format to CAF v2 format converter for genomic assembly data" HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/" diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog index 8024f81e1..e36ad4701 100644 --- a/sci-biology/gbrowse/ChangeLog +++ b/sci-biology/gbrowse/ChangeLog @@ -1,7 +1,20 @@ -# ChangeLog for sci-biology/generic-genome-browser -# Copyright 2000-2010 Gentoo Foundation; Distributed under the GPL v2 +# ChangeLog for sci-biology/gbrowse +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $ +*gbrowse-2.38 (26 Jun 2011) + + 26 Jun 2011; Justin Lecher <jlec@gentoo.org> -gbrowse-2.26.ebuild, + -files/GBrowseInstall.pm-2.26.patch, + -files/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch, + -gbrowse-2.33.ebuild, -files/GBrowseInstall.pm-2.33.patch, + +gbrowse-2.38.ebuild, +files/GBrowseInstall.pm-2.38.patch: + Version Bump + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -gbrowse-1.70.ebuild, + -gbrowse-2.00.ebuild, gbrowse-2.26.ebuild, gbrowse-2.33.ebuild: + Cleaned ebuild, 'http://search.cpan.org/CPAN' found in thirdpartymirrors + 05 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: Version bump diff --git a/sci-biology/gbrowse/Manifest b/sci-biology/gbrowse/Manifest index 96f87cdb3..101b58a14 100644 --- a/sci-biology/gbrowse/Manifest +++ b/sci-biology/gbrowse/Manifest @@ -1,13 +1,11 @@ -AUX GBrowseInstall.pm-2.26.patch 2647 RMD160 5acd26d95bf0c26edb0f816e840b43ef99a88ea3 SHA1 39362a38cff41097ead8c49de5eaf94d77c59f02 SHA256 1aee7359bc1b036f5d214975a5ea2395a507f04b0ee839ed3a1543a0ab4fb3c6 -AUX GBrowseInstall.pm-2.33.patch 1278 RMD160 96c7f2c66537c6e01cf2619018f608607c0927dc SHA1 a3cb874018d2c7a5acf34381971cc09d83a13f73 SHA256 5a1018f582c2e0ffca034d04ce73f678dd879d90932e4e89ea664c7c113f4b7c -AUX GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch 1001 RMD160 6784a8d01714be237247d56df13de96681f3aea5 SHA1 55c3eac7eb1e11c766b8d430c7dd36336347ef50 SHA256 a25f49dba6609a25c799d0290713038b608f8aef1a4275eff5f1f12e5225a19a +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +AUX GBrowseInstall.pm-2.38.patch 1278 RMD160 96c7f2c66537c6e01cf2619018f608607c0927dc SHA1 a3cb874018d2c7a5acf34381971cc09d83a13f73 SHA256 5a1018f582c2e0ffca034d04ce73f678dd879d90932e4e89ea664c7c113f4b7c AUX gbrowse-slave.default 210 RMD160 77245190ab0d3a543f3103bb6f21864f73ea1cde SHA1 a19d60edd3fdc1f059ed8fa58f7e91fc47ec92dc SHA256 e4e6d68ade29681f442b2e1c7f8abbc7ff3255b3b8db3c59ed6368ba561d7d66 AUX gbrowse-slave.init.d 2196 RMD160 8b565d1be23c89cbae0f9fd5cd2201f47a564b94 SHA1 738bc8f06486a0e6caa72642f79f9b7dbb356524 SHA256 de511a92757153ee648eb6cd39e3c69c1e30fa2c2ed406f24c08571c72609219 AUX gbrowse.conf.vhosts.d 740 RMD160 e24f5132e37a84dd0bb9a39e2de99cd11d260844 SHA1 2c44fdcf04bef92eb6210d4e6667b994e5643a13 SHA256 8acd5a067ab3dd42cff0ab7cb0d783b2409ccb872590eba32ea55d4929f65f21 -DIST GBrowse-2.00.tar.gz 3844690 RMD160 f3856ca620d8adc10172d8dfb644dfbbd25cbf88 SHA1 9d78393ca21d2569a975cfff7588cb7fe62d1082 SHA256 62c96ae1c6c1494ff67fbea1fde0d80d5051705c22167a55db317a0d33b1b8ea -DIST GBrowse-2.26.tar.gz 11937473 RMD160 c2c9d988e3183637b0a97f00e8de1387ad107eab SHA1 3153afc0ef7e6ea8ca6879343028673fdb062501 SHA256 4ac5c0fd87c5ab64b3c52ebb51f51433cb8c6062fd80a56d3de91f24594d3a3f -DIST GBrowse-2.33.tar.gz 11915644 RMD160 0e2f054b4bcc2748895a856620af7e50f5e15038 SHA1 f31cbe960904b5a2ea4b7eae7a9d78baaf29fce0 SHA256 063114b844776a9500528437fb3dbc60f47a8ac380d910bd6b3148ec7cc0cc4b -DIST Generic-Genome-Browser-1.70.tar.gz 3331393 RMD160 056f72fc17bdbf803fce7e6bdde406566a80c204 SHA1 7a83abaedc4d2b061e1247972036025a713a845f SHA256 e08ef0d1ffff8186bffd30177808ad3dd7991a99abf3ea6350c8d487ba835486 +DIST GBrowse-2.38.tar.gz 11966992 RMD160 dde50d49ee1b228103dffc9701e450ac9e3be3cd SHA1 4228a4938cbdbc409ddb23f81cd3186cdf15391d SHA256 acf7d3d0f32d0138640b2773ed580572ff63d646d4538f354dec8986607aa275 DIST README-gff-files 5309 RMD160 8ba184fa8a6b921f925143cf53de06e3da353023 SHA1 ad2d2b3133c73a05ace4a0107ff1a3a4221bc8f8 SHA256 21f4f026b212698c5aac0e82045670f8397ab50fdfe74b938fcbc71a1d36c82a DIST Refseq_Genome_TBLASTX.tar.gz 56482234 RMD160 e188d9dfe12bed3fd299be4625f7e658f54bb8c4 SHA1 72ec3de9b9ca0e10c2dd8dcda24f9be74f98cf09 SHA256 7036bdd9aefbf44e384df83f4c1e973c1ab3eac8fe74b37499c4a3f1c55a18af DIST fly.fasta.gz 37349852 RMD160 4bedfcc5d0ea3d325f3d3e446713251a8ce34ca3 SHA1 8f2c7a2f24dbab0f27c73009fe51efb8f41d6769 SHA256 892ed03e17edd3469f1ed00cb9967fb905bbac57c1cb7858667381f34a6bfeea @@ -18,9 +16,13 @@ DIST worm.fasta.gz 30593662 RMD160 674ef3d09cdfaa5d748f18c0e769f0a5ca3d48cf SHA1 DIST worm.gff.gz 65789458 RMD160 ddced7c965963ce41a10bdecae949731ed305121 SHA1 ccfb0f287e27ff7849b099c81d811f468a7e617c SHA256 afd63c65c3fdb0ba8a1cf455bd4477a2d5d27d5b0e88c6a5a10d156d0567374f DIST yeast.fasta.gz 3801757 RMD160 5545054cf6ffa5381c7992141144107076fdf62e SHA1 c36fddc5fd2c79e01292f66644088654304bc438 SHA256 bf51cbced31aa6a30bca43cc72fdb53194fbb403407e2ebb9d70c901ab072e6d DIST yeast.gff.gz 249814 RMD160 64538d18de23d930915938bd00ae4a94a52f3960 SHA1 ec753b1ae409e1377f568531a53be8985a7bfa2e SHA256 20c93e6ba9457896a693d13e8fd8fa00d77acbb55aee9b19a31c2b29c4b7e9b1 -EBUILD gbrowse-1.70.ebuild 1670 RMD160 e9bf6980abebabc6ff807ea3c682a3988d0a5f14 SHA1 0413b93216348184e79b3feea36cd68618bed688 SHA256 ecb0b9290e48b82a0d29520d8418593db7baa564bb3731ed7ed808f1b4b5ff3f -EBUILD gbrowse-2.00.ebuild 1932 RMD160 5a0d15a10c2f6f9e4ac1f60ce048efcd2311cdb4 SHA1 186d5a91fbae9b6894091ac376addb84784d6a03 SHA256 21b035ef921900bc893a4de0fe123b6192860265e0594b73723c24b03dd5a23c -EBUILD gbrowse-2.26.ebuild 6959 RMD160 a3b966bad08410ea7e619b4cb6497a78836c6094 SHA1 ec109df87df0cfc0d72c35a1c662b2c85f495a10 SHA256 3020b2c5953e7bc02ed1e1e98a8b63bb69feda55101725d019201e748394e5b6 -EBUILD gbrowse-2.33.ebuild 6207 RMD160 20e3780fe421c5b83add7a52d4629a9e169994f0 SHA1 cb5c80a5e6f558f41b71a832e4384501a846271d SHA256 1dfe2823194c4ac30ffd2530d96c04c4a533592fbd1a6931584c0af74422cca3 -MISC ChangeLog 1985 RMD160 9695d7522c6165b842087b67938629377f9cc82b SHA1 3edd2e74f9b26289d95ad7609b838edb3ccb9561 SHA256 76c1d0553f09390397af4354dc653677f25d06828e42e57a60b2f35a869222ac +EBUILD gbrowse-2.38.ebuild 6136 RMD160 9da72299772f44f80f9a653840fa167d04c1d3e5 SHA1 9a65efd853905e653b5a781128e45cc0e00e611a SHA256 db0cc819ad165d509c935e4cef5be3ee1f47d0e0a0a1ecb697ef6290b7259ad5 +MISC ChangeLog 2531 RMD160 a666bbe4d2aa432f678eb56d321db77686990b45 SHA1 d4950185a71e503373f25af3466fd876d2996249 SHA256 2c805b6e02263dfaf7b2c87ed68e8da2a8cbc1d23409968c36037105338038da MISC metadata.xml 572 RMD160 bc941571413238acb3d77e61d49b959737ed4f5a SHA1 0c05303509c0e2dd21b37fc93c936809db49e530 SHA256 89b9964a9404a95dbb622a91735348da8e66d34d7dd7e7f144ed8c0159c43e31 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4G56MACgkQgAnW8HDreRaXVQCgwiv8qpUdbIu7rc522SjTi/lq +cQ4AoMbh/D6qOR+v7qwowOCzPKmTktJb +=+CVr +-----END PGP SIGNATURE----- diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.26.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.26.patch deleted file mode 100644 index 4c17f8d9a..000000000 --- a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.26.patch +++ /dev/null @@ -1,72 +0,0 @@ ---- install_util/GBrowseInstall.pm.ori 2010-11-27 12:01:58.000000000 +0100 -+++ install_util/GBrowseInstall.pm 2010-11-27 12:02:15.000000000 +0100 -@@ -436,8 +436,8 @@ - $self->ownership_warning($databases,$user); - } - -- chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); -- $self->fix_selinux; -+ # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); -+ # $self->fix_selinux; - - my $base = basename($self->install_path->{htdocs}); - ---- install_util/GBrowseInstall.pm.ori 2011-02-14 13:39:46.000000000 +0100 -+++ install_util/GBrowseInstall.pm 2011-02-14 13:41:50.000000000 +0100 -@@ -438,25 +438,25 @@ - $gid =~ /^(\d+)$/; - $gid = $1; - -- unless (chown $uid,$gid,$tmp) { -- $self->ownership_warning($tmp,$user); -- } -+# unless (chown $uid,$gid,$tmp) { -+# $self->ownership_warning($tmp,$user); -+# } - - my $htdocs_i = File::Spec->catfile($self->install_path->{htdocs},'i'); - my $images = File::Spec->catfile($tmp,'images'); - my $htdocs = $self->install_path->{htdocs}; -- chown $uid,-1,$htdocs; -- { -- local $> = $uid; -- symlink($images,$htdocs_i); # so symlinkifowner match works! -- } -- chown $>,-1,$self->install_path->{htdocs}; -+# chown $uid,-1,$htdocs; -+# { -+# local $> = $uid; -+# symlink($images,$htdocs_i); # so symlinkifowner match works! -+# } -+# chown $>,-1,$self->install_path->{htdocs}; - - my $databases = $self->install_path->{'databases'}; - -- unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) { -- $self->ownership_warning($databases,$user); -- } -+# unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) { -+# $self->ownership_warning($databases,$user); -+# } - - # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); - # $self->fix_selinux; ---- install_util/GBrowseInstall.pm.ori 2011-02-14 13:50:41.000000000 +0100 -+++ install_util/GBrowseInstall.pm 2011-02-14 13:51:46.000000000 +0100 -@@ -470,11 +470,11 @@ - my @inc = map{"-I$_"} split ':',$self->added_to_INC; - system $perl,@inc,$metadb_script; - -- if (Module::Build->y_n( -- "It is recommended that you restart Apache. Shall I try this for you?",'y' -- )) { -- system "sudo /etc/init.d/apache2 restart"; -- } -+# if (Module::Build->y_n( -+# "It is recommended that you restart Apache. Shall I try this for you?",'y' -+# )) { -+# system "sudo /etc/init.d/apache2 restart"; -+# } - - print STDERR "\n***INSTALLATION COMPLETE***\n"; - print STDERR "Load http://localhost/$base for demo and documentation.\n"; diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.33.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.38.patch index e91fe1634..e91fe1634 100644 --- a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.33.patch +++ b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.38.patch diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch deleted file mode 100644 index 0dde70406..000000000 --- a/sci-biology/gbrowse/files/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch +++ /dev/null @@ -1,21 +0,0 @@ ---- install_util/GBrowseInstall.pm.ori 2011-05-11 04:10:08.000000000 +0200 -+++ install_util/GBrowseInstall.pm 2011-05-11 04:10:26.000000000 +0200 -@@ -463,12 +463,12 @@ - - my $base = basename($self->install_path->{htdocs}); - -- # Configure the databases, if needed. -- print STDERR "Updating user account database...\n"; -- my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl"); -- my $perl = $self->perl; -- my @inc = map{"-I$_"} split ':',$self->added_to_INC; -- system $perl,@inc,$metadb_script; -+# # Configure the databases, if needed. -+# print STDERR "Updating user account database...\n"; -+# my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl"); -+# my $perl = $self->perl; -+# my @inc = map{"-I$_"} split ':',$self->added_to_INC; -+# system $perl,@inc,$metadb_script; - - # if (Module::Build->y_n( - # "It is recommended that you restart Apache. Shall I try this for you?",'y' diff --git a/sci-biology/gbrowse/gbrowse-1.70.ebuild b/sci-biology/gbrowse/gbrowse-1.70.ebuild deleted file mode 100644 index 9bf0f47ce..000000000 --- a/sci-biology/gbrowse/gbrowse-1.70.ebuild +++ /dev/null @@ -1,68 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/generic-genome-browser-1.58.ebuild,v 1.9 2007/07/29 17:07:38 phreak Exp $ - -EAPI="2" - -inherit perl-module webapp - -MY_P="Generic-Genome-Browser-${PV}" - -DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages" -HOMEPAGE="http://gmod.org" -SRC_URI="mirror://sourceforge/gmod/${MY_P}.tar.gz" - -LICENSE="Artistic" -# webapp ebuilds do not set SLOT -KEYWORDS="~x86 ~amd64" -IUSE="-minimal" # lwp moby scf - -S="${WORKDIR}/${MY_P}" - -# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/libwww-perl, LWP -DEPEND=">=dev-lang/perl-5.8.8 - >=sci-biology/bioperl-1.6 - >=dev-perl/GD-2.07 - dev-perl/IO-String - virtual/perl-Digest-MD5 - >=dev-perl/CGI-Session-4.03 - dev-perl/Statistics-Descriptive - >=dev-perl/Bio-Graphics-1.97" -RDEPEND="${DEPEND} - >=www-servers/apache-2.0.47 - >=virtual/perl-CGI-2.56 - dev-perl/DBI - dev-perl/DBD-mysql - dev-perl/Class-Base - dev-perl/Text-Shellwords - !minimal? ( - dev-perl/XML-Parser - dev-perl/XML-Writer - dev-perl/XML-Twig - dev-perl/XML-DOM - dev-perl/GD-SVG - dev-perl/Bio-Das - )" - -src_configure() { - webapp_src_preinst - perl Makefile.PL \ - HTDOCS="${D}/${MY_HTDOCSDIR}" \ - CGIBIN="${D}/${MY_HTDOCSDIR}/cgi-bin" \ - CONF="${D}/etc" \ - PREFIX="${D}/usr" \ - PACKAGE_DIR="${D}" \ - INSTALLDIRS=vendor \ - GBROWSE_ROOT=gbrowse \ - DESTDIR="${ROOT}" \ - || die -} - -src_install() { - mydoc="Changes README TODO INSTALL" - perl-module_src_install - - # TODO: write our own readme - webapp_postinst_txt en "${S}/INSTALL" - webapp_src_install -} diff --git a/sci-biology/gbrowse/gbrowse-2.00.ebuild b/sci-biology/gbrowse/gbrowse-2.00.ebuild deleted file mode 100644 index cce42a39b..000000000 --- a/sci-biology/gbrowse/gbrowse-2.00.ebuild +++ /dev/null @@ -1,76 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/generic-genome-browser-1.58.ebuild,v 1.9 2007/07/29 17:07:38 phreak Exp $ - -EAPI="2" - -inherit perl-module webapp - -MY_P="GBrowse-${PV}" - -DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages" -HOMEPAGE="http://gmod.org" -SRC_URI="mirror://sourceforge/gmod/${MY_P}.tar.gz" - -LICENSE="Artistic" -# webapp ebuilds do not set SLOT -KEYWORDS="~x86 ~amd64" -IUSE="-minimal" # lwp moby scf - -S="${WORKDIR}/${MY_P}" - -# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10) -DEPEND=">=dev-lang/perl-5.8.8 - >=sci-biology/bioperl-1.6 - >=dev-perl/GD-2.07 - dev-perl/IO-String - virtual/perl-Digest-MD5 - >=dev-perl/CGI-Session-4.03 - dev-perl/Statistics-Descriptive - >=dev-perl/Bio-Graphics-1.97 - dev-perl/JSON - dev-perl/libwww-perl" -RDEPEND="${DEPEND} - >=www-servers/apache-2.0.47 - dev-perl/DBI - || ( dev-perl/DBD-Pg dev-perl/DBD-mysql ) - !minimal? ( - dev-perl/File-NFSLock - dev-perl/FCGI - perl-core/Math-BigInt - dev-perl/Digest-SHA1 - dev-perl/Crypt-SSLeay - dev-perl/Net-SMTP-SSL - dev-perl/GD-SVG - dev-perl/Net-OpenID-Consumer - virtual/perl-DB_File - dev-perl/DB_File-Lock - )" - -src_prepare() { - sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die -} - -src_configure() { - webapp_src_preinst - perl Makefile.PL \ - HTDOCS="${D}/${MY_HTDOCSDIR}" \ - CGIBIN="${D}/${MY_HTDOCSDIR}/cgi-bin" \ - CONF="${D}/etc" \ - PREFIX="${D}/usr" \ - PACKAGE_DIR="${D}" \ - INSTALLDIRS=vendor \ - GBROWSE_ROOT=gbrowse \ - DESTDIR="${ROOT}" \ - || die -} - -src_install() { - mydoc="Changes README TODO INSTALL" - perl-module_src_install - - # TODO: write our own readme - webapp_postinst_txt en "${S}/INSTALL" - webapp_src_install -# find "${D}" -type f | xargs sed -i "s|${D}||" || die -} diff --git a/sci-biology/gbrowse/gbrowse-2.26.ebuild b/sci-biology/gbrowse/gbrowse-2.26.ebuild deleted file mode 100644 index 89000cfd4..000000000 --- a/sci-biology/gbrowse/gbrowse-2.26.ebuild +++ /dev/null @@ -1,167 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ -EAPI="2" - -inherit perl-module webapp - -MY_P="GBrowse-${PV}" - -DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages" -HOMEPAGE="http://gmod.org" -SRC_URI="mirror://sourceforge/gmod/${MY_P}.tar.gz - test? ( http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2 - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )" - -LICENSE="Artistic" -# webapp ebuilds do not set SLOT -KEYWORDS="~x86 ~amd64" -IUSE="-minimal svg test" # lwp moby scf - -S="${WORKDIR}/${MY_P}" - -# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10) -# TODO: make sure www-servers/apache +cgi -DEPEND=">=dev-lang/perl-5.8.8 - dev-perl/Capture-Tiny - >=sci-biology/bioperl-1.6 - >=dev-perl/GD-2.07 - dev-perl/IO-String - virtual/perl-Digest-MD5 - >=dev-perl/CGI-Session-4.03 - dev-perl/Statistics-Descriptive - >=dev-perl/Bio-Graphics-1.97 - dev-perl/JSON - dev-perl/libwww-perl - svg? ( dev-perl/GD-SVG )" - -# TODO: based on the following message in apache/error_log the list of deps should be longer -# GBROWSE NOTICE: To enable PDF generation, please enter the directory "/home/httpd" and run the commands: "sudo mkdir .inkscape .gnome2" and "sudo chown apache .inkscape .gnome2". To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse_details/yeast?ref=chrII;start=90739;end=92028;name=YBL069W;class=Sequence;feature_id=881;db_id=annotations%3Adatabase - -# * Bio::DB::BigFile is not installed -# * Bio::DB::Sam is not installed -# * DBD::Pg is not installed - -RDEPEND="${DEPEND} - >=www-servers/apache-2.0.47 - www-apache/mod_fastcgi - dev-perl/DBI - || ( dev-perl/DBD-Pg dev-perl/DBD-mysql ) - !minimal? ( - dev-perl/File-NFSLock - dev-perl/FCGI - perl-core/Math-BigInt - perl-core/Math-BigInt-FastCalc - dev-perl/Math-BigInt-GMP - dev-perl/Digest-SHA1 - dev-perl/Crypt-SSLeay - dev-perl/Net-SMTP-SSL - dev-perl/Net-OpenID-Consumer - virtual/perl-DB_File - dev-perl/DB_File-Lock - dev-perl/GD-SVG - dev-perl/Text-Shellwords - dev-perl/XML-Twig - dev-perl/XML-DOM - dev-perl/XML-Writer - dev-perl/XML-Parser - dev-perl/Bio-Das - dev-perl/Text-Shellwords - )" - -src_prepare() { - sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die - sed -i 's/process_/bp_process_/g' INSTALL || die - epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to patch" - epatch "${FILESDIR}"/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl"${PV}".pm.patch || die "Failed to patch" -} - -src_configure() { - # GBROWSE_ROOT is the root path in SRC_URI to be prepended - # /usr/share/webapps/gbrowse/2.03/htdocs/etc/gbrowse/GBrowse.conf - - # if we use CONF="${D}${MY_HTDOCSDIR}"/etc/gbrowse the the install process - # will not find currently installed config files and therefore place *.conf - # files into "{$S}"/blib/conf/*.conf instead of creating "{$S}"/blib/conf/*.conf.new - webapp_src_preinst - perl Makefile.PL \ - HTDOCS="${MY_HTDOCSDIR}" \ - CGIBIN="${MY_HTDOCSDIR}"/cgi-bin \ - CONF="${MY_HTDOCSDIR}"/etc/gbrowse \ - PACKAGE_DIR="${D}" \ - INSTALLDIRS=vendor \ - GBROWSE_ROOT="gbrowse" \ - DESTDIR="${D}" \ - DATABASES="/var/www/gbrowse2/databases/" \ - TMP="/var/tmp/gbrowse2" \ - INSTALLETC="n" \ - INSTALLCONF="n" \ - WWWUSER="apache" \ - DO_XS=1 \ - NONROOT=1 \ - || die - - #sed -i 's#DBI:SQLite:#DBI:SQLite:'${D}'#' "${S}"/install_util/GBrowseInstall.pm || die - #sed -i 's#DBI:SQLite:#DBI:SQLite:'${D}'#' "${S}"/conf/GBrowse.conf || die - #sed -i 's#/var/www/gbrowse2/databases/#'${D}'/var/www/gbrowse2/databases/#' "${S}"/_build/build_params - #sed -i 's#/var/www/gbrowse2/databases/#'${D}'/var/www/gbrowse2/databases/#' "${S}"/_build/config_data - #sed -i 's#/var/www/gbrowse2/databases/#'${D}'/var/www/gbrowse2/databases/#' "${S}"/_build/runtime_params -} - -src_install() { - mydoc="Changes README TODO INSTALL" - perl-module_src_install - - # TODO: write our own readme - webapp_src_preinst - webapp_postinst_txt en "${S}"/INSTALL || die - webapp_src_install - - # should create a /etc/init.d/ startup script based on this - # /var/tmp/portage/sci-biology/gbrowse-2.03/work/GBrowse-2.03/etc/init.d/gbrowse-slave - - # pre-create the directory so we can force its owner later on - mkdir -p "${D}"/var/www/gbrowse2/databases || die - chown -R apache.apache "${D}"/var/www/gbrowse2/databases || die - mkdir -p "${D}"/var/www/localhost/htdocs/gbrowse || die - - ln -s "${D}"/var/tmp/gbrowse2/images "${D}"/var/www/localhost/htdocs/gbrowse/i || die - - einfo "Probably you want to install a cron job to remove the generated temporary images:" - einfo "find /var/tmp/gbrowse2/images -type f -atime +20 -print -exec rm {}" - - einfo "Make sure you compiled apache with +cgi and copy ${FILESDIR}/gbrowse.conf.vhosts.d to /etc/apache2/vhosts.d/" - - sed -i "s#"${D}"##g" "${S}"/install_util/GBrowseInstall.pm || die - sed -i "s#"${D}"##" "${S}"/blib/conf/GBrowse.conf* - sed -i 's#DBI:SQLite:'${D}'/var/www/gbrowse2/databases/#DBI:SQLite:/var/www/gbrowse2/databases/#' "${S}"/install_util/GBrowseInstall.pm || die -} - -pkg_postinst() { - webapp_pkg_postinst || die "webapp_pkg_postinst failed" - - einfo "Please run gbrowse_metadb_config.pl to upate SQlite flatfiles or the live database" - einfo "This was disabled by "${FILESDIR}"/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm.patch" -} - -src_test() { - mysql -uroot -p password -e 'create database yeast' - mysql -uroot -p password -e 'grant all privileges on yeast.* to gbrowse@localhost' - mysql -uroot -p password -e 'grant file on *.* to gbrowse@localhost' - mysql -uroot -p password -e 'grant select on yeast.* to nobody@localhost' - - cd /usr/portage/distfiles || die - gzip -d yeast.fasta.gz || die - gzip -d yeast.gff.gz || die - #gzip -d fly.fasta.gz - #gzip -d fly.gff.gz - bp_bulk_load_gff.pl -d yeast -fasta yeast.fasta yeast.gff || die -} diff --git a/sci-biology/gbrowse/gbrowse-2.33.ebuild b/sci-biology/gbrowse/gbrowse-2.38.ebuild index e2bcfc3be..9cc3ce479 100644 --- a/sci-biology/gbrowse/gbrowse-2.33.ebuild +++ b/sci-biology/gbrowse/gbrowse-2.38.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI="2" @@ -7,21 +7,23 @@ inherit perl-module webapp MY_P="GBrowse-${PV}" -DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages" -HOMEPAGE="http://gmod.org" +DESCRIPTION="Display of genomic annotations on interactive web pages" +HOMEPAGE="http://gmod.org/" # mirror://sourceforge/gmod/${MY_P}.tar.gz -# http://search.cpan.org/CPAN/authors/id/L/LD/LDS/GBrowse-2.33.tar.gz -SRC_URI="http://search.cpan.org/CPAN/authors/id/L/LD/LDS/${MY_P}.tar.gz - test? ( http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2 - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )" +# mirror://cpan/authors/id/L/LD/LDS/GBrowse-2.33.tar.gz +SRC_URI=" + mirror://cpan/authors/id/L/LD/LDS/${MY_P}.tar.gz + test? ( + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2 + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )" LICENSE="Artistic" # webapp ebuilds do not set SLOT @@ -54,7 +56,6 @@ DEPEND=" # * Bio::DB::Sam is not installed # * DBD::Pg is not installed - RDEPEND="${DEPEND} >=www-servers/apache-2.0.47 www-apache/mod_fastcgi diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest index f0061cf81..18b89f258 100644 --- a/sci-biology/mira/Manifest +++ b/sci-biology/mira/Manifest @@ -1,8 +1,11 @@ +AUX libtool.m4.patch 355 RMD160 3c6386ced352747fa274c1a6f70e5cff9969a050 SHA1 dddbed5cd51bb86209e6108d542fdb13c0481341 SHA256 58065ce386008c4843ea42e30d406257e25656ae7870c6e6f65735f1a84326ed AUX mira-3.0.0-asneeded.patch 1468 RMD160 5ad66bd3a1861ef984af4fb2b527755fd8901440 SHA1 f17e537e98f77eeaaf7502894f8383dd96c588bc SHA256 17dec784921baccf2c515f7c269209b5cdeb23143b3412e8ad967e74682ee71f AUX mira_left_clip.readpool.C.patch 1036 RMD160 ed1fb66fb936958df8fb5ffe830bd367e2a68a19 SHA1 8a3f0cd92c86adf6131dc5a8e52ab9de5bbbb6e0 SHA256 63e027658e7ce7418641477294af473a7c9253c20374e6918254f8e2404d1212 DIST mira-3.2.1.17.tar.bz2 9611305 RMD160 b9a124c572763fa8923c1b1ee5b12e54b881b67c SHA1 a2731ba4da5af9f0c575ff355a481ea0190dd898 SHA256 2d79ebbbfc6801ff500cabd79cd63358e50296fbdcd1aed4028ea52503d76f8c +DIST mira-3.2.1.18.tar.bz2 9614978 RMD160 39e7afc6dfe1b97b5b7b2201b7b970ca9eb3222a SHA1 07d8c98c7234919411f55e915d1f8f483eb1e883 SHA256 9e05870da7828981a265fa79b717858959538593b4985cd4244fe4b16ebf709a DIST mira-3.2.1.tar.bz2 9626154 RMD160 b998226fe4ea0efbe6023dac8b073af1782167b9 SHA1 432d1ecd2acb62a8584f29a10b55943165cd0586 SHA256 86a2c00d182573008ef41f7725aec72ea69756ea9f3dc7e798a7d253a47f8bd7 DIST mira_3rdparty_17-04-2010.tar.bz2 31296 RMD160 888a38f865963b3109d3a331604e079010b55d81 SHA1 5f2fbe3e2e1bb5c5de44d414963e57b8dbcf760c SHA256 ec2c77508d75b7c28d3d26137ab69648b1ed653af93d486245ad0e4624e332b2 -EBUILD mira-3.2.1-r2.ebuild 1625 RMD160 0cbe968caf227b01a11d1c96ffb5f4706d47a542 SHA1 446130eb9a3a900147ae4d01cbe821f007987814 SHA256 659a3a9c1a9d60c64c990e9899e8d571676dd3aafc648867d49846fe04fe43e2 -EBUILD mira-3.2.1.17-r1.ebuild 1985 RMD160 58d00d38cee873a88779206cf6813a0be759756e SHA1 7649c28cd3f21b5eca0233686efbc9833268ef04 SHA256 dc47d01298cc48d80698869fade197462f2e7ed319d7fe70c5e932838288acc8 +EBUILD mira-3.2.1-r2.ebuild 1664 RMD160 be0cc98203c14df172ceeaa8594ba81a9dda8040 SHA1 2742271c780c73dd05e0549486e63bea1683631c SHA256 fbd24bad5133e64bc38055b038ae6093b2fcc024d66c04dffa2ca2f5d067d39c +EBUILD mira-3.2.1.17-r1.ebuild 1751 RMD160 02c62d754aac7173934f587ffe3bb005c893b5cd SHA1 269b9c4dd37e4568b9c3506c2e12fdb3d56dd12b SHA256 f80038926310bb16f9f9d6bf99e662b96a0f53195462bd59ea6130b76393ae06 +EBUILD mira-3.2.1.18.ebuild 1788 RMD160 ab3617a08c3daf04ccb737588856952dec8ee593 SHA1 bdecda83ee1cf7185b1b98c38fd8497a3dbfa1ce SHA256 535493e9bf59476570cd979176d58a2a03d25b5776459ad61eaa82113415efaa MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 diff --git a/sci-biology/mira/files/libtool.m4.patch b/sci-biology/mira/files/libtool.m4.patch new file mode 100644 index 000000000..9cfaeef09 --- /dev/null +++ b/sci-biology/mira/files/libtool.m4.patch @@ -0,0 +1,13 @@ +--- config/m4/libtool.m4.ori 2011-06-22 12:28:14.000000000 +0200 ++++ config/m4/libtool.m4 2011-06-22 12:28:39.000000000 +0200 +@@ -88,10 +88,6 @@ + # This can be used to rebuild libtool when needed + LIBTOOL_DEPS="$ltmain" + +-# Always use our own libtool. +-LIBTOOL='$(SHELL) $(top_builddir)/libtool' +-AC_SUBST(LIBTOOL)dnl +- + _LT_SETUP + + # Only expand once: diff --git a/sci-biology/mira/mira-3.2.1-r2.ebuild b/sci-biology/mira/mira-3.2.1-r2.ebuild index a4de8cce4..c110959eb 100644 --- a/sci-biology/mira/mira-3.2.1-r2.ebuild +++ b/sci-biology/mira/mira-3.2.1-r2.ebuild @@ -31,6 +31,7 @@ src_prepare() { epatch "${FILESDIR}"/${PN}-3.0.0-asneeded.patch # http://sourceforge.net/apps/trac/mira-assembler/ticket/47 epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch + epatch "${FILESDIR}"/libtool.m4.patch AT_M4DIR="config/m4" eautoreconf } diff --git a/sci-biology/mira/mira-3.2.1.17-r1.ebuild b/sci-biology/mira/mira-3.2.1.17-r1.ebuild index 9fe96ff69..04b37674c 100644 --- a/sci-biology/mira/mira-3.2.1.17-r1.ebuild +++ b/sci-biology/mira/mira-3.2.1.17-r1.ebuild @@ -16,9 +16,7 @@ SRC_URI="mirror://sourceforge/mira-assembler/${P}.tar.bz2 LICENSE="GPL-2" SLOT="0" IUSE="" -KEYWORDS="" -# masked because of 'libtool: Version mismatch error. This is libtool 2.4, but the definition of this LT_INIT comes from libtool 2.2.6b. You should recreate aclocal.m4 with macros from libtool 2.4 and run autoconf again.', dyeing at src/examples_programming/ -#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" CDEPEND=">=dev-libs/boost-1.41.0-r3 dev-util/google-perftools" @@ -33,6 +31,7 @@ src_prepare() { epatch "${FILESDIR}"/${PN}-3.0.0-asneeded.patch # http://sourceforge.net/apps/trac/mira-assembler/ticket/47 epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch + epatch "${FILESDIR}"/libtool.m4.patch AT_M4DIR="config/m4" eautoreconf } diff --git a/sci-biology/mira/mira-3.2.1.18.ebuild b/sci-biology/mira/mira-3.2.1.18.ebuild new file mode 100644 index 000000000..3ea8ce177 --- /dev/null +++ b/sci-biology/mira/mira-3.2.1.18.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +MIRA_3RDPARTY_PV="17-04-2010" + +inherit autotools base multilib + +DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina" +HOMEPAGE="http://www.chevreux.org/projects_mira.html" +SRC_URI="mirror://sourceforge/mira-assembler/${P}.tar.bz2 + mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" + +CDEPEND=">=dev-libs/boost-1.41.0-r3 + dev-util/google-perftools" +DEPEND="${CDEPEND} + dev-libs/expat" +RDEPEND="${CDEPEND} + sci-biology/smalt-bin + sci-biology/ssaha2-bin" + +src_prepare() { + find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die + epatch "${FILESDIR}"/${PN}-3.0.0-asneeded.patch + # http://sourceforge.net/apps/trac/mira-assembler/ticket/47 + epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch + epatch "${FILESDIR}"/libtool.m4.patch + AT_M4DIR="config/m4" eautoreconf + #epatch "${FILESDIR}"/libtool.patch +} + +src_configure() { + econf \ + --with-boost="${EPREFIX}"/usr/$(get_libdir) \ + --with-boost-libdir="${EPREFIX}"/usr/$(get_libdir) \ + --with-boost-thread=boost_thread-mt +} + +src_compile() { + base_src_compile + # TODO: resolve docbook incompatibility for building docs + if use doc; then emake -C doc clean docs || die "This will probably die because upstream did not imrove re-genartion of the docs yet."; fi +} + +src_install() { + einstall || die + dodoc AUTHORS GETTING_STARTED NEWS README* HELP_WANTED THANKS INSTALL + find doc/docs/man -type f | xargs doman + find doc/docs/texinfo -type f | xargs doinfo + dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} +} diff --git a/sci-biology/mrbayes/ChangeLog b/sci-biology/mrbayes/ChangeLog index f2ce30569..7c54e60cf 100644 --- a/sci-biology/mrbayes/ChangeLog +++ b/sci-biology/mrbayes/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/mrbayes -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/ChangeLog,v 1.19 2008/06/11 18:10:48 ken69267 Exp $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> mrbayes-3.1.2-r1.ebuild, + metadata.xml: + RDEPEND is not explicitly assigned -> fixed + 27 Jun 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> mrbayes-3.1.2-r1.ebuild: QA fixes diff --git a/sci-biology/mrbayes/Manifest b/sci-biology/mrbayes/Manifest index 96782ec95..96dcbdf8a 100644 --- a/sci-biology/mrbayes/Manifest +++ b/sci-biology/mrbayes/Manifest @@ -1,25 +1,15 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX mb_readline_312.patch 1108 RMD160 5901513567ef2198b4c9c1baeb1ecc295af3eee8 SHA1 c5526cf58fe15cb22c401de19de7056a66c37414 SHA256 6d7566cbe59eee9881b41a21ea561fd610816df768bb8fda42ef4435c84f5f22 DIST mrbayes-3.1.2.tar.gz 545968 RMD160 b90b9406f34806bcd18bc49dc998b7ed444e93c3 SHA1 db73f53361688e1451ec155ccbdd130c3f889817 SHA256 c60253de1980c9f0a0eb684fffe7ba428fda7c39a3edcb6acf384b5e1443f2f4 -EBUILD mrbayes-3.1.2-r1.ebuild 1290 RMD160 ea28415fb61052376cb5f969d45fbf6f02e629a8 SHA1 95c96987a36c751e9e71d7c75409df4d3ca85586 SHA256 37fe5ed6d86c80bf35a54fe930166b0710625e3336d52421ad9acd3f5a6a46f9 -MISC ChangeLog 2968 RMD160 09b289d34cd8679cbee91b06804825d0af85d41b SHA1 0a04a57f0930a2813d3c423a38a7d65c994a4504 SHA256 a5a75909a551d9064baa39f8417fab021d253947715d9bac92d1a491cd3ea8fb -MISC metadata.xml 730 RMD160 46eda6e69c53a0e301343cfc645c343c5aa9fdd6 SHA1 06e33f8fa877635c7e771e74e3edeb8cba146fb3 SHA256 fe9b9273c53a7c502d6688d63557fe603f63a47c8ff17355b9db7cdc0b78f446 +EBUILD mrbayes-3.1.2-r1.ebuild 1316 RMD160 ded04cf025556ded7cd1c34f18c283dde70ae5d4 SHA1 a660680775448d9f313e7040eed5436eab172fba SHA256 fd3653ddccf4faa0dddfb502b8d0ea59cfcf7a2788dc1906b58607638de716c6 +MISC ChangeLog 3103 RMD160 46686758663971c63f4504b3f6765112da662bee SHA1 fd287ecf0d712fd76267cf73d9a96bd554acff40 SHA256 644b6d880b1e332e61ba896a2e86347b42f18ced23f83922f3cdd674df2f786b +MISC metadata.xml 732 RMD160 c9c73ca971a4c88f5054245bde9585b694924fe8 SHA1 7d2195b53ba6e6a30f6a3c84072d62a0822faf06 SHA256 b1d3e5fd22ec3c1cd73e0a1de97d994690145894dbe024cf66e91e56ee3925eb -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) +Version: GnuPG v2.0.17 (GNU/Linux) -iQIcBAEBAgAGBQJMJ67+AAoJENwGBM22xffezFoP/0wwMAdnLe3KZUO7TNg4rc+X -l8Ll2kWUJ64krvyMucKDqQ9ZCK9XR4R7q97p+pOaFjno0sVqk9kBpRzvMewMryxH -HeKV/7CrCkCKVjNdSxH0G2ZT7pPfCEM394rrFMucVqZvyb76azhT1VDizGWQJkDj -2e3WPAuiULklW4kHaD6R0TDSGhpnptLyu7UQLIsiF3anReMS/QSX7XwM5rAejfkw -hoa6+iiQYe2+sI9RWmj9KvjQNwv5tEt8FlMqTA26S4RL6ceTb8QPRWFE6AZWPCid -HCj0oWIQIBAptkhCKKoqE423u9EIGfN9r1zRgVX+gLr+2gC0aA9Ag1kB9ZF384jp -MmxgDwVjKZqT4qw5HRXMMLGPqL2RxsaGb9ZD50ucE0Eb6zaWHexCXEOiS0Ik4lXV -/Idl1KUCl7wQpewZO0HPniaVDz/waKVlcawCSNFzAX/1mLtthtvwyFoN4hCn/mth -6CTY7itGOneSZmoxabbOOXb2aKMNsrkvRxL+kVWzn+375Cibc2tAZF5VgTDucq4D -XE09M/0qNRdThzvIyBW1wpEWLZynIpCqjoA53JwaMF8wBiF61NNL0JPYCGQD5v+r -SOvYIOceuMb1ifmuZjcZMNV8dGmleGel5/4YCvYjARjHxBa/QtQnUDHJ1tMhi5nN -W+b5ci6syZqZ8VMLuXIL -=Toc4 +iEYEAREIAAYFAk4F5kUACgkQgAnW8HDreRbrcQCgwaM3QhDgQSOnyM7DN3nNw1Bt +tkoAn0eVMkH/raPdh1MAcoQEK0QFsI3d +=OD3v -----END PGP SIGNATURE----- diff --git a/sci-biology/mrbayes/metadata.xml b/sci-biology/mrbayes/metadata.xml index d33282dbb..102b1ec80 100644 --- a/sci-biology/mrbayes/metadata.xml +++ b/sci-biology/mrbayes/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-biology</herd> -<longdescription> + <herd>sci-biology</herd> + <longdescription> MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild index 4c65db786..f29856adf 100644 --- a/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild +++ b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild @@ -1,25 +1,28 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/mrbayes-3.1.2.ebuild,v 1.7 2008/06/11 18:10:48 ken69267 Exp $ -inherit eutils toolchain-funcs mpi +inherit eutils mpi toolchain-funcs DESCRIPTION="Bayesian Inference of Phylogeny" -LICENSE="GPL-2" HOMEPAGE="http://mrbayes.csit.fsu.edu/" SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" SLOT="0" -IUSE="mpi readline" +LICENSE="GPL-2" KEYWORDS="~amd64 ~x86" +IUSE="mpi readline" -DEPEND="mpi? ( $(mpi_pkg_deplist) ) +DEPEND=" + mpi? ( $(mpi_pkg_deplist) ) readline? ( sys-libs/readline )" +RDEPEND="${DEPEND}" src_unpack() { unpack ${A} cd "${S}" - sed -e "s:OPTFLAGS ?= -O3:CFLAGS = ${CFLAGS}:" \ + sed \ + -e "s:OPTFLAGS ?= -O3:CFLAGS = ${CFLAGS}:" \ -e "s:CC = gcc:CC = $(tc-getCC):" \ -e "s:CC = mpicc:CC = $(mpi_pkg_cc):" \ -e "s:LDFLAGS =:LDFLAGS ?=:" \ diff --git a/sci-biology/newbler/ChangeLog b/sci-biology/newbler/ChangeLog deleted file mode 100644 index d651a0680..000000000 --- a/sci-biology/newbler/ChangeLog +++ /dev/null @@ -1,7 +0,0 @@ -# ChangeLog for sci-biology/newbler -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 01 May 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: - New package, ebuild written by me - diff --git a/sci-biology/newbler/Manifest b/sci-biology/newbler/Manifest deleted file mode 100644 index f96dc4334..000000000 --- a/sci-biology/newbler/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -DIST offInstrumentApps_2.0.01.10-64.tar.gz 80613372 RMD160 2d638e058a11117dbe23d27902eb28fd60f4a1aa SHA1 eec7a881ed2f8dbf277233660f38d7ab72a0ccc6 SHA256 349b8065a323526fce6394c9cdc3959f68d2a6690cdcbbd3aca6a08729ff5bd0 -EBUILD newbler-2.0.01.10.ebuild 965 RMD160 65c9abe5b1ad755a0fbf150382bc51f34d1ecdef SHA1 2328164d1387fd2a0813745946ee9ba1bce65ec7 SHA256 0c1aec58f151d423c9b8176204c1e3d1c0f50e3c893eddcab9174aff3af02dfb -MISC ChangeLog 218 RMD160 a71508054d9bb459a17ec6888fe33656bcdf296c SHA1 46f02a60127224aaa3f3722b650bb4a7fc6d8f8b SHA256 c2b76d95cbde1128dc5b36fc466ccfd1c08179ac6b28d6b897fbd10fe974221a -MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 diff --git a/sci-biology/newbler/metadata.xml b/sci-biology/newbler/metadata.xml deleted file mode 100644 index 3302123e5..000000000 --- a/sci-biology/newbler/metadata.xml +++ /dev/null @@ -1,9 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer> - <email>weaver@gentoo.org</email> - <name>Andrey Kislyuk</name> - </maintainer> - <herd>sci-biology</herd> -</pkgmetadata> diff --git a/sci-biology/newbler/newbler-2.0.01.10.ebuild b/sci-biology/newbler/newbler-2.0.01.10.ebuild deleted file mode 100644 index a044ea826..000000000 --- a/sci-biology/newbler/newbler-2.0.01.10.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/amos-2.0.8.ebuild,v 1.2 2009/03/15 17:58:50 maekke Exp $ - -EAPI="2" - -DESCRIPTION="Roche 454 pyrosequencing assembler" -HOMEPAGE="http://www.454.com/products-solutions/analysis-tools/index.asp" -SRC_URI="offInstrumentApps_2.0.01.10-64.tar.gz" - -LICENSE="newbler" -SLOT="0" -IUSE="" -KEYWORDS="~amd64" - -DEPEND="app-arch/rpm" -RDEPEND=">=virtual/jre-1.6" - -RESTRICT="fetch" - -S="${WORKDIR}/offInstrumentApps_${PV}-64" - -pkg_nofetch() { - einfo "Please visit ftp://ftp.454.com/ and obtain the file" - einfo "\"${SRC_URI}\", then place it in ${DISTDIR}" -} - -src_prepare() { - sed -i -e "s|/etc/profile.d|${D}/etc/profile.d|" "${S}/INSTALL" || die -} - -src_install() { - echo -e "\n\n${D}/opt/454\nno\n" | "${S}"/INSTALL || die - rm -rf "${D}/opt/454/jre" || die - echo "PATH=/opt/454/bin" > "${S}/99${PN}" - doenvd "${S}/99${PN}" -} diff --git a/sci-biology/nrcl/ChangeLog b/sci-biology/nrcl/ChangeLog new file mode 100644 index 000000000..86d3e89ec --- /dev/null +++ b/sci-biology/nrcl/ChangeLog @@ -0,0 +1,14 @@ +# ChangeLog for sci-biology/nrcl +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/110625-build.patch, + -files/0.1-build.patch: + mv 0.1-build.patch 110625-build.patch + +*nrcl-110625 (25 Jun 2011) + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/0.1-build.patch, + -nrcl-0.1.ebuild, +nrcl-110625.ebuild: + Cleaned ebuild + diff --git a/sci-biology/nrcl/Manifest b/sci-biology/nrcl/Manifest index 41cd6ca97..ca68de31d 100644 --- a/sci-biology/nrcl/Manifest +++ b/sci-biology/nrcl/Manifest @@ -1,4 +1,16 @@ -DIST cdbfasta.tar.gz 59735 RMD160 c90e0ede03a01bf2da77f9beaa3c97fa7e46ff2a SHA1 2419421ab1d753d3bb8778c92236da74fee30526 SHA256 68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c -DIST nrcl.tar.gz 14782 RMD160 c3e122ccd1d30e25c278e9f0a7928ab6d1a1e451 SHA1 8650388bbf27640f5b2c261e1eafe286e34adcb4 SHA256 8795728d60416d1329a352479335b084d3627af8e6ba5e4ba043041970886f46 -EBUILD nrcl-0.1.ebuild 1223 RMD160 163f2e14872074fb445b8941038e417d22d1193a SHA1 c842fdc757a6b984a724981155d122ce5d178cb7 SHA256 cbb0f36d07ede9150b1b8b37558f83a7c4a3692fcaf0344f58db61ef85c7efda +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +AUX 110625-build.patch 1184 RMD160 adbdf53d27d41f8095492ed28a437d6b64191886 SHA1 09bbb5e77185ecc7cde825d395a908600bda794d SHA256 eee62d137ca6359c2a2f614054d55afb711291dffc239c62a5cc07f01b9f293e +DIST gclib.tar.gz 82727 RMD160 f12395354b47980577e9d83cc100a6bf6568bd33 SHA1 4c433e6a87663211dc00e2d855a11a058e5b6b48 SHA256 0c7f21fc92b033cd442b672e9014e3ffb9f2de97769ca525715692ed9359439b +DIST nrcl-110625.tar.gz 14782 RMD160 c3e122ccd1d30e25c278e9f0a7928ab6d1a1e451 SHA1 8650388bbf27640f5b2c261e1eafe286e34adcb4 SHA256 8795728d60416d1329a352479335b084d3627af8e6ba5e4ba043041970886f46 +EBUILD nrcl-110625.ebuild 695 RMD160 0fc3eaa7b2e44a6f75a02338c0cdb46c40e746f4 SHA1 9abbc7a63ee83d05d6b4a0beda87a5d49a2805dd SHA256 c26a2521b93facdb258ddafd778cff41e77dfe7fcc8807c36e678ba01ee13846 +MISC ChangeLog 416 RMD160 3fefc5209cdc0714d17cc9185ccded1f231ca510 SHA1 437674e0eb6356d52606daff5b8059ba5afe95e8 SHA256 2e65db83ad0ada4de4aab7272adeb63ead6a90ced9a2447502797153ede09b58 MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F+ssACgkQgAnW8HDreRaX4gCfe65l6YTL5Wxo5Q5l8PPYUpQS +qlMAnib37W1cGwHoiSaqMRe4yhukXkhW +=ShI9 +-----END PGP SIGNATURE----- diff --git a/sci-biology/nrcl/files/110625-build.patch b/sci-biology/nrcl/files/110625-build.patch new file mode 100644 index 000000000..64fa893a4 --- /dev/null +++ b/sci-biology/nrcl/files/110625-build.patch @@ -0,0 +1,48 @@ + Makefile | 18 +++++++++--------- + 1 files changed, 9 insertions(+), 9 deletions(-) + +diff --git a/Makefile b/Makefile +index 6d5d68f..30a1019 100644 +--- a/Makefile ++++ b/Makefile +@@ -11,23 +11,23 @@ SYSTYPE := $(shell uname) + + # C compiler + +-CC := g++ +-CFLAGS = -O2 -Wall ${SEARCHDIRS} -fno-exceptions -fno-rtti -fno-strict-aliasing -D_REENTRANT ++CXX ?= g++ ++CXXFLAGS += -Wall ${SEARCHDIRS} -fno-exceptions -fno-rtti -fno-strict-aliasing -D_REENTRANT + + %.o : %.c +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + +-%.o : %.cc +- ${CC} ${CFLAGS} -c $< -o $@ ++%.o : %.CXX ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.C +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.cpp +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.cxx +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + # C/C++ linker + +@@ -39,7 +39,7 @@ LOADLIBES := + all: nrcl + + nrcl: ./nrcl.o ${GCLDIR}/GBase.o ${GCLDIR}/GStr.o ${GCLDIR}/GArgs.o +- ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} ++ ${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} + + # target for removing all object files + diff --git a/sci-biology/nrcl/nrcl-0.1.ebuild b/sci-biology/nrcl/nrcl-0.1.ebuild deleted file mode 100644 index 6f44a0b17..000000000 --- a/sci-biology/nrcl/nrcl-0.1.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -DESCRIPTION="Containment clustering and layout utility for processing pairwise alignments from TIGR Gene Indices project tools" -HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/" -SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz - ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="${DEPEND}" - -S=${WORKDIR} - -src_prepare() { - # we need gclib from cdbfasta.tar.gz bundle which has fewer files than tgi_cpp_library.tar.gz wbut has e.g. GStr.h - sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' "${S}"/${PN}/Makefile || die "Failed to run sed" - sed -i 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#' "${S}"/"${PN}"/Makefile || die - cd ${PN} || die - ln -s ../cdbfasta/gcl . || die "Cannot make a softlink" -} - -src_compile() { - cd ${PN} || die - emake || die "emake failed in "${S}"/${PN}" -} - -src_install() { - cd ${PN} || die - dobin ${PN} || die "Failed to install ${PN} binary" - newdoc README README.${PN} -} diff --git a/sci-biology/nrcl/nrcl-110625.ebuild b/sci-biology/nrcl/nrcl-110625.ebuild new file mode 100644 index 000000000..1a599dd4c --- /dev/null +++ b/sci-biology/nrcl/nrcl-110625.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Containment clustering and layout utility for processing pairwise alignments" +HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/" +SRC_URI=" + ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz -> ${P}.tar.gz + ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/gclib.tar.gz -> gclib.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +S="${WORKDIR}"/${PN} + +src_prepare() { + epatch "${FILESDIR}"/${PV}-build.patch + tc-export CXX +} + +src_install() { + dobin ${PN} + dodoc README +} diff --git a/sci-biology/proda/ChangeLog b/sci-biology/proda/ChangeLog index 7ca249fa6..46cc65f5c 100644 --- a/sci-biology/proda/ChangeLog +++ b/sci-biology/proda/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/proda -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: + Fixed herd entry in metadata.xml + 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +proda-1.0.ebuild: Mass import from sunrise diff --git a/sci-biology/proda/Manifest b/sci-biology/proda/Manifest index a08c08aed..22b6dfbbc 100644 --- a/sci-biology/proda/Manifest +++ b/sci-biology/proda/Manifest @@ -1,4 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST proda_1_0.tar.gz 38868 RMD160 b024496c935cebb74d50479d8cdeacce820358b1 SHA1 44303e1639b5c52278758d23d149ef1c434593a4 SHA256 439a93bf35e1a29ac1d5dde51e61f2cb174618596afaaaaa27d33a8ea1868a08 EBUILD proda-1.0.ebuild 703 RMD160 46c755309e2925f3ebcc6ede718cd7b3d38c8469 SHA1 e9c55e5782f00660795cb8749c5373f4c1124bbd SHA256 8c454b35cafb73ca9c77662f922cff590498d39dafca97bbf2a4803e8d8c6524 -MISC ChangeLog 335 RMD160 913d0c1816d44d2b575580909498c0ab71a2d16c SHA1 0d4cb7d8379e35695dc9f76df4d6120bd1d7cbbc SHA256 c9a0ed83283201f9dc4e644e83668eb162f6be98cf08e9b55c3df4748355c85d -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 +MISC ChangeLog 432 RMD160 3c15b5841844c425a4bed5010bed995e637c9916 SHA1 63f329133582b2ea3d9e5e801e876090d831142a SHA256 4c837b94fcb8b4fd0725d7c8a7ed3acb821aa566e8da1ba8013d6bca1844cef0 +MISC metadata.xml 158 RMD160 9b441c987a00c5a66c06850c0d587a2abd70893c SHA1 7a8997eb2fc55fda167d3e95cdffb43c8f817fdf SHA256 dae7918daac89b300804812d32584889aa1c4e8b9edeced06006900494457a6d +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4Fkb0ACgkQgAnW8HDreRbkZgCgk8Gs1Q0Tp6imzxlr2e85PGAf +iHsAn34iEA5K4GDFRQ/F33g8Uo4pXePG +=iiaD +-----END PGP SIGNATURE----- diff --git a/sci-biology/proda/metadata.xml b/sci-biology/proda/metadata.xml index 7e3286984..897aa2e6b 100644 --- a/sci-biology/proda/metadata.xml +++ b/sci-biology/proda/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>maintainer-wanted</herd> + <herd>sci</herd> </pkgmetadata> diff --git a/sci-biology/seqclean/ChangeLog b/sci-biology/seqclean/ChangeLog new file mode 100644 index 000000000..b03c585ea --- /dev/null +++ b/sci-biology/seqclean/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/seqclean +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*seqclean-110625 (25 Jun 2011) + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -seqclean-0.1.ebuild, + +seqclean-110625.ebuild, +files/seqclean-110625-build.patch: + Cleaned ebuild + diff --git a/sci-biology/seqclean/Manifest b/sci-biology/seqclean/Manifest index bd0c55a33..4249af699 100644 --- a/sci-biology/seqclean/Manifest +++ b/sci-biology/seqclean/Manifest @@ -1,5 +1,17 @@ -DIST mdust.tar.gz 7526 RMD160 c04a6ba5a56724bfee70b8fe31f0bf4132b74885 SHA1 8885f206d61a76c6623c4115af02793bb52911c4 SHA256 9722806920fc6772dc92f99e7a59554c5f7c35b596dca0df9ed03ff2e5c6440d -DIST seqcl_scripts.tar.gz 14840 RMD160 5e97c43b1e6b77aef48366d7802e04c9ec0b8054 SHA1 cf487d2321f21894014f361a2a6839bef6e85f24 SHA256 bc8bba4fcff5e012a3eafe48fc5d5f843e9689aad5f063c595bede9ac5b27e43 -DIST trimpoly.tar.gz 12747 RMD160 a3b22f501a8291a015a0a85efc4afa812a1d1439 SHA1 bde5b24e1cbc522609ae660343bbe4084da330f0 SHA256 e6dfb3cb6b8e205a5627d20029207cd0a87be5095b4c556b6b3f716fba287666 -EBUILD seqclean-0.1.ebuild 1842 RMD160 48be3cec69ecede8e90ccd2297ca279ccca51937 SHA1 2b54b2ec16b1689429a5e7638a9a753574c3d5b8 SHA256 449489cce79b04376fc5a27010eb2c9a4cd07cc372b3937a127b422d8078beb3 +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +AUX seqclean-110625-build.patch 2984 RMD160 cdce63f091a24cdad8452969e8ae7304ec783fcc SHA1 3daf1144a675bb228584389dbc9be2865ada4947 SHA256 443bd8ae25894bf1d63c72370caaf48fb2ebff825a26f4fff313ee0f181f832a +DIST mdust-110625.tar.gz 7526 RMD160 c04a6ba5a56724bfee70b8fe31f0bf4132b74885 SHA1 8885f206d61a76c6623c4115af02793bb52911c4 SHA256 9722806920fc6772dc92f99e7a59554c5f7c35b596dca0df9ed03ff2e5c6440d +DIST seqcl_scripts-110625.tar.gz 14840 RMD160 5e97c43b1e6b77aef48366d7802e04c9ec0b8054 SHA1 cf487d2321f21894014f361a2a6839bef6e85f24 SHA256 bc8bba4fcff5e012a3eafe48fc5d5f843e9689aad5f063c595bede9ac5b27e43 +DIST trimpoly-110625.tar.gz 12747 RMD160 a3b22f501a8291a015a0a85efc4afa812a1d1439 SHA1 bde5b24e1cbc522609ae660343bbe4084da330f0 SHA256 e6dfb3cb6b8e205a5627d20029207cd0a87be5095b4c556b6b3f716fba287666 +EBUILD seqclean-110625.ebuild 1373 RMD160 0c84d786c58625deea76f46789a71c22ebd0f44f SHA1 80afe2eb6f076926be19fa2343a2542f18e86913 SHA256 f27cf254f1a03650024d617f4678f3339505da19f268369ec9428577857db4e7 +MISC ChangeLog 303 RMD160 a33093fdf475cfa7a02a48646f05fd9446067cb9 SHA1 554321e80db0da43ee4f1e6740fc019e30a1e88b SHA256 98ec118f2981a85729c45bba185175374120c6caecb5af3f460711edc653fc86 MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F+98ACgkQgAnW8HDreRa7/QCeOpQW46JXR8Me2PxOWFPXNA/7 +AMMAnAofQaaVdRqV1GtUgp2q/NR8WM+d +=XQtZ +-----END PGP SIGNATURE----- diff --git a/sci-biology/seqclean/files/seqclean-110625-build.patch b/sci-biology/seqclean/files/seqclean-110625-build.patch new file mode 100644 index 000000000..b5797618f --- /dev/null +++ b/sci-biology/seqclean/files/seqclean-110625-build.patch @@ -0,0 +1,135 @@ + mdust/Makefile | 18 +++++++++--------- + mdust/fastafile.c | 3 ++- + mdust/mdust.c | 1 + + trimpoly/Makefile | 16 ++++++++-------- + 4 files changed, 20 insertions(+), 18 deletions(-) + +diff --git a/mdust/Makefile b/mdust/Makefile +index 81bf4e9..0c75e69 100644 +--- a/mdust/Makefile ++++ b/mdust/Makefile +@@ -1,40 +1,40 @@ + # Useful directories + + # Directories to search for header files +-SEARCHDIRS := -I. -I- ++SEARCHDIRS := -I. -iquote + + + #SYSTYPE := $(shell uname) + +-CC := gcc +-CFLAGS = -O2 -Wall ${SEARCHDIRS} -D_REENTRANT ++CC ?= gcc ++CFLAGS += ${SEARCHDIRS} -D_REENTRANT ++CXXFLAGS += ${SEARCHDIRS} -D_REENTRANT + + %.o : %.c + ${CC} ${CFLAGS} -c $< -o $@ + + %.o : %.cc +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.C +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.cpp +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.cxx +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + # C/C++ linker + + LINKER := gcc +-LDFLAGS = + LOADLIBES := + + .PHONY : all + all: mdust + + mdust: ./mdust.o ./dust.o ./fastafile.o +- ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} ++ ${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} + + # target for removing all object files + +diff --git a/mdust/fastafile.c b/mdust/fastafile.c +index 6c14b99..5f70f14 100644 +--- a/mdust/fastafile.c ++++ b/mdust/fastafile.c +@@ -1,7 +1,8 @@ + #include <stdio.h> + #include <ctype.h> + #include <malloc.h> +- ++#include <string.h> ++#include <stdlib.h> + #include "fastafile.h" + + +diff --git a/mdust/mdust.c b/mdust/mdust.c +index f2bae99..c3ee686 100644 +--- a/mdust/mdust.c ++++ b/mdust/mdust.c +@@ -1,6 +1,7 @@ + #include <stdlib.h> + #include <stdio.h> + #include <ctype.h> ++#include <string.h> + #include "dust.h" + #include "fastafile.h" + +diff --git a/trimpoly/Makefile b/trimpoly/Makefile +index 84db22d..71145c2 100644 +--- a/trimpoly/Makefile ++++ b/trimpoly/Makefile +@@ -3,28 +3,28 @@ + # Directories to search for header files + SEARCHDIRS := -I. + +-CC := gcc +-CFLAGS = -O2 -Wall ${SEARCHDIRS} -D_REENTRANT ++CC ?= gcc ++CFLAGS += ${SEARCHDIRS} -D_REENTRANT ++CXXFLAGS += ${SEARCHDIRS} -D_REENTRANT + + %.o : %.c + ${CC} ${CFLAGS} -c $< -o $@ + + %.o : %.cc +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.C +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.cpp +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.cxx +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + # C/C++ linker + + LINKER := gcc +-LDFLAGS = + LOADLIBES = + SYSTYPE := $(shell uname) + #ifeq ($(SYSTYPE), Linux) +@@ -37,7 +37,7 @@ SYSTYPE := $(shell uname) + all: trimpoly + + trimpoly: ./trimpoly.o color_c.o +- ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} ++ ${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} + + # target for removing all object files + diff --git a/sci-biology/seqclean/seqclean-0.1.ebuild b/sci-biology/seqclean/seqclean-0.1.ebuild deleted file mode 100644 index eae3ef686..000000000 --- a/sci-biology/seqclean/seqclean-0.1.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -DESCRIPTION="Trimpoly and mdust for trimming and validation of ESTs/DNA sequences, low quality and low-complexity sequences with two binaries" -HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software" -for i in seqclean/{seqcl_scripts,mdust,trimpoly}; do - SRC_URI="${SRC_URI} ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/${i}.tar.gz" -done - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="dev-lang/perl - sci-biology/ncbi-tools" -RDEPEND="${DEPEND}" - -S=${WORKDIR} - -src_unpack() { - unpack {seqcl_scripts,mdust,trimpoly}.tar.gz -} - -src_prepare() { - # disable the necessity to install Mailer.pm with this tool - einfo "Disabling mailer feature within seqclean" - sed -i 's/use Mailer;/#use Mailer;/' "${S}"/"${PN}"/"${PN}" || die - - for i in mdust trimpoly; do - sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' "${S}"/${i}/Makefile || die "Failed to run sed" - sed -i "s#-I-#-iquote#" "${S}"/${i}/Makefile || die "Failed to run sed" - done -} - -src_compile() { - # seqclean/ contains just perl scripts, no need to compile - for i in mdust trimpoly; do - cd "${S}"/${i} || die "Failed to cd "${S}"/${i}" - emake || die "emake failed in "${S}"/${i}" - done -} - -src_install() { - dobin seqclean/{seqclean,cln2qual,bin/seqclean.psx} || die "Failed to install the perl-based scripts" - newdoc seqclean/README README.seqclean - for i in mdust trimpoly; do - dobin ${i}/${i} || die "Failed to install ${i} binary" - done - - einfo "Optionally, you might want to download UniVec from NCBI if you do not have your own" - einfo "fasta file with vector sequences you want to remove from sequencing" - einfo "reads. See http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html" -} diff --git a/sci-biology/seqclean/seqclean-110625.ebuild b/sci-biology/seqclean/seqclean-110625.ebuild new file mode 100644 index 000000000..45085b137 --- /dev/null +++ b/sci-biology/seqclean/seqclean-110625.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Trimpoly and mdust for trimming and validation of ESTs/DNA sequences" +HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/" +for i in seqcl_scripts mdust trimpoly; do + SRC_URI="${SRC_URI} ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/seqclean/${i}.tar.gz -> ${i}-${PV}.tar.gz" +done + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=" + dev-lang/perl + sci-biology/ncbi-tools" +RDEPEND="${DEPEND}" + +S=${WORKDIR} + +src_prepare() { + # disable the necessity to install Mailer.pm with this tool + einfo "Disabling mailer feature within seqclean" + sed -i 's/use Mailer;/#use Mailer;/' "${S}"/"${PN}"/"${PN}" || die + + epatch "${FILESDIR}"/${P}-build.patch + + tc-export CC CXX +} + +src_compile() { + for i in mdust trimpoly; do + LDLFAGS="${LDFLAGS}" \ + emake -C "${S}"/${i} + done +} + +src_install() { + dobin seqclean/{seqclean,cln2qual,bin/seqclean.psx} + newdoc seqclean/README README.seqclean + for i in mdust trimpoly; do + dobin ${i}/${i} + done + + einfo "Optionally, you might want to download UniVec from NCBI if you do not have your own" + einfo "fasta file with vector sequences you want to remove from sequencing" + einfo "reads. See http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html" +} diff --git a/sci-biology/sequin/ChangeLog b/sci-biology/sequin/ChangeLog index 7b5a10528..ca9c2b059 100644 --- a/sci-biology/sequin/ChangeLog +++ b/sci-biology/sequin/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/sequin -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: + Fixed herd entry in metadata.xml + 19 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: New package, ebuild written by me diff --git a/sci-biology/sequin/Manifest b/sci-biology/sequin/Manifest index d606d2794..6d4f5ce54 100644 --- a/sci-biology/sequin/Manifest +++ b/sci-biology/sequin/Manifest @@ -1,5 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST sequin-20090722-x86.tar.gz 5999782 RMD160 44ce5da6cebdc0cbf385982dc721acf5c0ab982d SHA1 80804ec6fe8beac91f3b56f4ca8dcdee43dddb16 SHA256 f12fe7fa084a1d19a75e67cfcb4027cefb91c819b7c6219499072a87f00bdc51 DIST sequin-20090722-x86_64.tar.gz 6911415 RMD160 69da84f677231a5f98ae80de87681355810f31da SHA1 84b4bb6e5a93534fcb580c2e92050885f3a72c69 SHA256 338de057edf9c14e911f69c372c9480675c2b5a4b24efed605dcbdf7e8e4d486 EBUILD sequin-20090722.ebuild 918 RMD160 61377e7367be0ef84a8d56fa6759dd4d796083dd SHA1 1de1bbc623f981a9f6e7915110f8b1de4e20fbc9 SHA256 a8e7d9d4e52be5e5662a8f67f515368610dcf0b3879f1e015b3ab80ed8f83c45 -MISC ChangeLog 217 RMD160 f99bc54f2f294bf99eb980b779503328d14dc9bf SHA1 84777dfb9a8770ee62cb07508be4d7f1c1f0f2e8 SHA256 ae0d741bd69f675ac6fbc8b45fe81d4fbeb770a4ff4ffabf2d85969e8a70592e -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 +MISC ChangeLog 314 RMD160 eedb349e22d5bdbda160c8847026f629e0c2dd8e SHA1 a827628c2054151ba73a37a8d958e64e3defb371 SHA256 a0177570f06b4c8482c41c213ef9284a5c7feb9008c0b0871be168c1eae2fc78 +MISC metadata.xml 158 RMD160 9b441c987a00c5a66c06850c0d587a2abd70893c SHA1 7a8997eb2fc55fda167d3e95cdffb43c8f817fdf SHA256 dae7918daac89b300804812d32584889aa1c4e8b9edeced06006900494457a6d +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4FkdsACgkQgAnW8HDreRZrxACgu4X2EJXZJ2q+eZM0Sa0m+mT4 +oxAAnjsZD1+LIAWcqg2CaTnRBUy2BNwa +=iDtV +-----END PGP SIGNATURE----- diff --git a/sci-biology/sequin/metadata.xml b/sci-biology/sequin/metadata.xml index 7e3286984..897aa2e6b 100644 --- a/sci-biology/sequin/metadata.xml +++ b/sci-biology/sequin/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>maintainer-wanted</herd> + <herd>sci</herd> </pkgmetadata> diff --git a/sci-biology/sff_dump/ChangeLog b/sci-biology/sff_dump/ChangeLog new file mode 100644 index 000000000..a9d53a380 --- /dev/null +++ b/sci-biology/sff_dump/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/sff_dump +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> sff_dump-1.04.ebuild: + Some ebuild cleaning + diff --git a/sci-biology/sff_dump/Manifest b/sci-biology/sff_dump/Manifest index b0cb07b6a..f38058e05 100644 --- a/sci-biology/sff_dump/Manifest +++ b/sci-biology/sff_dump/Manifest @@ -1,3 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + DIST sff_dump-1.04.tgz 55640 RMD160 4a83c4dd8427e101d15e28987434638408a6eb83 SHA1 ad2854724029ad476fe1719d6953cc9a58338f5f SHA256 94bfeb55bc146f2e0183a0b85622e3fa19772d4d2fb324332d72f4cc5a4104ba -EBUILD sff_dump-1.04.ebuild 726 RMD160 38282c68b9ad8d2cee6a231ce2e1588c21821457 SHA1 b08fdad83744f79b57f42eed3c81284dcbe61866 SHA256 1284a3166910f60acb0b9632151b321335a6007e85e06359f9260b0e5c333e62 -MISC metadata.xml 261 RMD160 ce19afc5fdd536a9eadb35a705f09613e3774e32 SHA1 b95b491e808c8dd5a106edae7e48af4f8d61f58a SHA256 e3766426d46af16432093cd9fb8a2df3862c77ef313ad175ca2ef60af5cee6f5 +EBUILD sff_dump-1.04.ebuild 647 RMD160 feb6f52b46dca5dd4cdb197d169e697c746f24ec SHA1 e679e8d5a0139cf70bc096f9e10850d85f7aa0cb SHA256 4ad2b394ec9bb964d23e5cfb73f6900b4b0a5f6d3c5f52bc9f775d43f78c5af8 +MISC ChangeLog 214 RMD160 dfffb7d56e057849bb97f3123e34689f4cc6cc92 SHA1 2ff87865fce952cc2733a9da6fcf0588cc82122b SHA256 64ffd81ec69e04e05f9c7ae23d0e8dd6b4ab1d358d8714a80c5dc0f37c9377e7 +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EzfwACgkQgAnW8HDreRaHkwCfVH92rc6/kopE+JHXd/80Tefl +IvgAnRaD/+vCOGHzdVV1aKPkVpSkzpQ1 +=plyn +-----END PGP SIGNATURE----- diff --git a/sci-biology/sff_dump/sff_dump-1.04.ebuild b/sci-biology/sff_dump/sff_dump-1.04.ebuild index 136e7276b..b0942764d 100644 --- a/sci-biology/sff_dump/sff_dump-1.04.ebuild +++ b/sci-biology/sff_dump/sff_dump-1.04.ebuild @@ -1,28 +1,30 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=4 -DESCRIPTION="Convert Roche SFF files to FASTA file format (alternative to sffdump from Roche and sff_extract from mira)" +inherit toolchain-funcs + +DESCRIPTION="Convert Roche SFF files to FASTA file format" HOMEPAGE="http://genome.imb-jena.de/software/roche454ace2caf" -SRC_URI="http://genome.imb-jena.de/software/roche454ace2caf/download/src/sff_dump-1.04.tgz" +SRC_URI="http://genome.imb-jena.de/software/roche454ace2caf/download/src/${P}.tgz" LICENSE="FLI-Jena" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND="" -RDEPEND="${DEPEND}" - src_prepare(){ - sed -i 's:^CC :#CC :' Makefile - sed -i 's:^LD :#LD :' Makefile - sed -i 's:^CFLAGS.*:CFLAGS+= -D__LINUX__ -Wcast-align:' Makefile - sed -i 's:^LDFLAGS=:#LDFLAGS=:' Makefile + sed \ + -e 's:^CC :#CC :' \ + -e 's:^LD :#LD :' \ + -e 's:^CFLAGS.*:CFLAGS+= -D__LINUX__ -Wcast-align:' \ + -e 's:^LDFLAGS=:#LDFLAGS=:' \ + -i Makefile || die + tc-export CC LD } src_install(){ - dobin sff_dump || die + dobin sff_dump } diff --git a/sci-biology/smalt-bin/ChangeLog b/sci-biology/smalt-bin/ChangeLog new file mode 100644 index 000000000..f3268fd32 --- /dev/null +++ b/sci-biology/smalt-bin/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/smalt-bin +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> smalt-bin-0.5.1.ebuild: + Cleaned ebuild and fixed LICENSE + diff --git a/sci-biology/smalt-bin/Manifest b/sci-biology/smalt-bin/Manifest index ff06d7e11..22371e482 100644 --- a/sci-biology/smalt-bin/Manifest +++ b/sci-biology/smalt-bin/Manifest @@ -1,3 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + DIST smalt-0.5.1.tgz 534824 RMD160 4c0a26256784f3eae2d3e9e62142faacb67c8e68 SHA1 070e548905306c8d41a5cf02e63287318e80e892 SHA256 c8bca18a7ded7ad4b7070be7478bd046cf2d6a0a81054dfd96ebdba65c0a49d0 -EBUILD smalt-bin-0.5.1.ebuild 731 RMD160 31c6e6d423edd8e3d4a0d34d71644dd86271a134 SHA1 8dcd74a972a0c41145dea31287918892a1459bf4 SHA256 f97a797c4191b588f66a16800d651ed37e60509b92a9e3b3fcd32b5d163fd4ac +EBUILD smalt-bin-0.5.1.ebuild 631 RMD160 da666c04658f52c2b682ab9d4b2d791a7121f5cb SHA1 4d5ab3db32936e0795f16385523ed94e1f18ff63 SHA256 aa1370a8a78759d3fe186537c86ac156a119371e8e4972b3becd11f37812b802 +MISC ChangeLog 229 RMD160 187bb30cd58954da377d4d8d45b7103eb234b489 SHA1 4c82cafe0d7b70539d9ce7d07ff3531ba213ab71 SHA256 b9e0b03040eeb118ec6b1423dd7a67125378b391bc75f96d9a1d91a69fe5ac8a MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F28EACgkQgAnW8HDreRZ1BQCgqgk9ZcB25V3lwOO9yfSKQW+X +Zs0AnRlU96l4nxvPH63mkqggHMAzBcMZ +=DNRi +-----END PGP SIGNATURE----- diff --git a/sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild b/sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild index 9124a6cbb..7566c2097 100644 --- a/sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild +++ b/sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild @@ -2,32 +2,24 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=4 -DESCRIPTION="Pairwise sequence alignment mapping DNA reads onto genomic reference, better over SSAHA2." +DESCRIPTION="Pairwise sequence alignment mapping DNA reads onto genomic reference, better over SSAHA2" HOMEPAGE="http://www.sanger.ac.uk/resources/software/smalt/" SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-"${PV}".tgz" -LICENSE="GRL" +LICENSE="as-is" SLOT="0" KEYWORDS="~x86 ~amd64" IUSE="" -DEPEND="" -RDEPEND="${DEPEND}" - S="${WORKDIR}"/smalt-"${PV}" src_install(){ - if use x86; then - newbin smalt_i386 smalt || die - fi - if use amd64; then - newbin smalt_x86_64 smalt || die - fi - if use ia64; then - newbin smalt_ia64 || die - fi - dodoc NEWS smalt_manual.pdf || die - doman smalt.1 || die + use x86 && newbin smalt_i386 smalt + use amd64 && newbin smalt_x86_64 smalt + use ia64 && newbin smalt_ia64 + + dodoc NEWS smalt_manual.pdf + doman smalt.1 } diff --git a/sci-biology/ssaha2-bin/ChangeLog b/sci-biology/ssaha2-bin/ChangeLog new file mode 100644 index 000000000..914725e6e --- /dev/null +++ b/sci-biology/ssaha2-bin/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/ssaha2-bin +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> ssaha2-bin-2.5.3.ebuild: + Cleaned ebuild and fixed LICENSE + diff --git a/sci-biology/ssaha2-bin/Manifest b/sci-biology/ssaha2-bin/Manifest index 148bbd392..548ad7100 100644 --- a/sci-biology/ssaha2-bin/Manifest +++ b/sci-biology/ssaha2-bin/Manifest @@ -1,7 +1,18 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + DIST samflag.c 2424 RMD160 a338182d756bdcd1214861d6273c0149df5e3177 SHA1 631282cc7fe88bac4f43011a0db09d9a1494859a SHA256 945958214ef1adc40029a6b3c323c37338e095e9e2bcbff5e5ec05aadbdb67d0 DIST ssaha2-manual.pdf 163188 RMD160 903bc1dc7f7bf89966f957c9df3c82128e233a53 SHA1 8e332b01628a3b64ea3dcc86d654a99d59277934 SHA256 1a0529168b71ac55e13b34264a854daa6a5dac9468f81ccb5b63bd5e1baafdbf DIST ssaha2_i686.tgz 288481 RMD160 0c493b917f40f5f259b6a6fe564ebc6a9e4409ec SHA1 b042e36c57f5e89098b6c5f07a2d646c02e76110 SHA256 7d173d763d9f685ef3d0075124bf8b763c6d2d3ed1a1f823bc66d6b6b029abed DIST ssaha2_ia64.tgz 458507 RMD160 8c3c821d292db94036f8d93342357ff0a8773bbe SHA1 a7ac847a64240f85eca3aff0df21bf9d339eed8f SHA256 3eb2a31559911f3ee87e11f3b977962da31b60c25ea0c9a064edfd1165b6b5dd DIST ssaha2_x86_64.tgz 287790 RMD160 93938da9898f30cf77f020329316228fd47ebe41 SHA1 d16d38e3bdab97994b4a70e4c0fc737a09b94d3a SHA256 0135ab2e285a898d450744b7c9d643efbeb6048783169a6647f310ce2e7b8138 -EBUILD ssaha2-bin-2.5.3.ebuild 1262 RMD160 316d8a8bfa9141159ce98215ee2a8ef121dfcb65 SHA1 7e4f63058267190dea68478ef20935bda63b848a SHA256 0929206dc3c0376c038507a234a2f54e5ad581514030e1131867c78cd2ddd07a +EBUILD ssaha2-bin-2.5.3.ebuild 1116 RMD160 af0f196ba6ce959ebf6d81115db2e9baa0190554 SHA1 79e1c04e3325d05dc0f914c14070955a1056cb4f SHA256 2c48c5fb6a7206930af612e88f52a1d5ce2537fb413fcb764060e4e9a2dcf68d +MISC ChangeLog 231 RMD160 5145398f2bfa105a4bdd2d361e32f7c51d15279e SHA1 0039c81fb8cfb17b60fbce912e03e9908042bdec SHA256 5aaf2c3745044bb045b9d1fc38249f74e135d690c9af921e030cf7a3606be2ef MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F3IUACgkQgAnW8HDreRbi3ACcCcSa7OHDWpL9VypnMDUMXsY+ +9CkAoJdyh2VAAqvtLbRkQ1PyZbAo3qNk +=hNec +-----END PGP SIGNATURE----- diff --git a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild index eaf02be74..34b63dd43 100644 --- a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild +++ b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild @@ -1,43 +1,34 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=4 inherit toolchain-funcs DESCRIPTION="SSAHA2: Sequence Search and Alignment by Hashing Algorithm" HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2" -SRC_URI="x86? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_i686.tgz ) - amd64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_x86_64.tgz ) - ia64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_ia64.tgz ) - ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/samflag.c - ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2-manual.pdf" - -LICENSE="GRL" +SRC_URI=" + x86? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_i686.tgz ) + amd64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_x86_64.tgz ) + ia64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_ia64.tgz ) + ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/samflag.c + ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2-manual.pdf" + +LICENSE="as-is" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND="" -RDEPEND="${DEPEND}" - -if use x86; then - S="${WORKDIR}"/ssaha2_v"${PV}"_i686 -fi -if use amd64; then - S="${WORKDIR}"/ssaha2_v"${PV}"_x86_64 -fi -if use ia64; then - S="${WORKDIR}"/ssaha2_v"${PV}"_ia64 -fi +use x86 && S="${WORKDIR}"/ssaha2_v"${PV}"_i686 +use amd64 && S="${WORKDIR}"/ssaha2_v"${PV}"_x86_64 +use ia64 && S="${WORKDIR}"/ssaha2_v"${PV}"_ia64 src_compile() { - $(tc-getCC) ${CFLAGS} -o samflag "${DISTDIR}"/samflag.c || die "Failed to compile samflags" + $(tc-getCC) ${CFLAGS} ${LDFLAGS} -o samflag "${DISTDIR}"/samflag.c || die "Failed to compile samflags" } src_install() { - dobin samflag ssaha2 ssaha2Build ssahaSNP || die "dobin failed" - dodoc README || die "dodoc failed" - dodoc "${DISTDIR}"/ssaha2-manual.pdf || die "Failed to install ssaha2-manual.pdf" + dobin samflag ssaha2 ssaha2Build ssahaSNP + dodoc README "${DISTDIR}"/ssaha2-manual.pdf } diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog new file mode 100644 index 000000000..1bf6d72fe --- /dev/null +++ b/sci-biology/staden/ChangeLog @@ -0,0 +1,16 @@ +# ChangeLog for sci-biology/staden +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 23 Jun 2011; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta8.ebuild, + staden-9999.ebuild: + Streamlined fortran-2 eclass usage + + 23 Jun 2011; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta8.ebuild, + staden-9999.ebuild: + Streamlined fortran-2 eclass usage + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta8.ebuild, + staden-9999.ebuild: + Added fortran-2.eclass support + diff --git a/sci-biology/staden/Manifest b/sci-biology/staden/Manifest index cc5fcf2b3..29d068a26 100644 --- a/sci-biology/staden/Manifest +++ b/sci-biology/staden/Manifest @@ -1,6 +1,17 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX rpath.patch 4178 RMD160 0d2c8778ff81bc122a9a8eb0b28e8a423172075d SHA1 1360f9cfaa02c15a8e7a9535ae1a02099501d1f5 SHA256 126be8f08307ebefb9312d4c1a63e8ee00ed4976440248fe1fe4d0ab7f2b4736 DIST staden-2.0.0b8.tar.gz 4312143 RMD160 68b91a80fae29e0bf8f7e6ca1c0781591113684c SHA1 742092ff7bfb5acd3376ac85d5ab50507d1dd02f SHA256 c13aa0c22dcac6b10d13501dcb630efad51d7c171968e0bb30113667b49cfa9d DIST staden_doc-2.0.0b8-src.tar.gz 3068758 RMD160 4844c3b5acc1ef16c438f66313e1a8b3c182edc2 SHA1 daa6f0702fa250817fbdd07f932cdf0ed993c6c2 SHA256 77dbf83ef674affb5ee21b6ac7875e8c36446092e076e4d99cffbc4b2220c65f -EBUILD staden-2.0.0_beta8.ebuild 2284 RMD160 0ca58b683a3d314035c6d2f122f071fdca2ee3df SHA1 7a9ddee9c21e17a2a2349038f5ca834a08a86e21 SHA256 1c745cff13c22949aaba0bbd6a389365d48474b3ae4415b91b272d755ad2accb -EBUILD staden-9999.ebuild 2287 RMD160 dcdc6a912ea5eb074241f5483e9ac1f5160ef280 SHA1 db4440eb263d1b692e8187e021b4e0bad95b6b74 SHA256 258092dc0cfe3fd1f3a01e0c48b930d101f86936aab7853a9dda9cdec3a599bf +EBUILD staden-2.0.0_beta8.ebuild 2171 RMD160 d081b577c1c77700864c0b52d2353a7446160345 SHA1 cd017670a4eccbd81e8cc36a228947d02c023ea7 SHA256 4ab13673c38cb2571a86f2e0db65cb82032298a5f04b4b2a330b81178987a8f4 +EBUILD staden-9999.ebuild 2033 RMD160 d420d1e7f1ba242e3d70f6e912c040648c02dd29 SHA1 f694feec606602f93b23f3dc2735b2e0794e003b SHA256 b917fc7dc9fe88ae3929032dc0509531c82ae6a9f2e2180fdd9e822678049205 +MISC ChangeLog 517 RMD160 57f23b63c7feec53fbfc53b50d72d9152522bdb0 SHA1 70db18c65e33bc2d20d80ea71c709fd2c576b8b5 SHA256 c2e03544f72470ecfd4b6f3e5e9de9375b64a159fd3ea81972b9cb849254b6d4 MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4DBiAACgkQgAnW8HDreRbZJwCfdd5Q1Y9W83ZzZx1PRSZfsVFP +goUAoNBW6lxxgve9xYwfaCvRsRrt7NiY +=Nos6 +-----END PGP SIGNATURE----- diff --git a/sci-biology/staden/staden-2.0.0_beta8.ebuild b/sci-biology/staden/staden-2.0.0_beta8.ebuild index a4e1e4737..f4f2411c3 100644 --- a/sci-biology/staden/staden-2.0.0_beta8.ebuild +++ b/sci-biology/staden/staden-2.0.0_beta8.ebuild @@ -4,40 +4,39 @@ EAPI=3 -inherit eutils flag-o-matic base +inherit base eutils flag-o-matic fortran-2 multilib -DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)." -HOMEPAGE="http://sourceforge.net/projects/staden" -SRC_URI="http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz - http://sourceforge.net/projects/staden/files/staden/2.0.0b8/staden_doc-2.0.0b8-src.tar.gz" +DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)" +HOMEPAGE="http://sourceforge.net/projects/staden/" +SRC_URI=" + http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz + http://sourceforge.net/projects/staden/files/staden/2.0.0b8/staden_doc-2.0.0b8-src.tar.gz" LICENSE="staden" SLOT="0" KEYWORDS="~x86 ~amd64" -IUSE="debug fortran X png curl tcl tk zlib" +IUSE="curl debug fortran png tcl tk X zlib" # either g77 or gfortran must be available # edit src/mk/linux.mk accordingly - # # this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058 # -# # -DEPEND=">=dev-lang/tk-8.4 - >=dev-lang/tcl-8.4 - dev-tcltk/tklib - >=sci-libs/io_lib-1.12.2 - >=sys-libs/zlib-1.2 - >=media-libs/libpng-1.2 - sci-biology/samtools - >=app-arch/xz-utils-4.999" - -# maybe we should depend on app-arch/lzma or app-arch/xz-utils? - -RDEPEND="tcl? ( >=dev-tcltk/itcl-3.2 ) - tk? ( >=dev-tcltk/itk-3.2 ) - >=dev-tcltk/iwidgets-4.0" +# +DEPEND=" + app-arch/xz-utils + dev-lang/tk + dev-tcltk/tklib + >=media-libs/libpng-1.2 + sci-biology/samtools + >=sci-libs/io_lib-1.12.2 + >=sys-libs/zlib-1.2 + virtual/fortran" +RDEPEND="${DEPEND} + >=dev-tcltk/iwidgets-4.0 + tcl? ( >=dev-tcltk/itcl-3.2 ) + tk? ( >=dev-tcltk/itk-3.2 )" S="${WORKDIR}"/staden-2.0.0b8-src @@ -54,11 +53,7 @@ src_configure(){ myconf=" --with-tklib=/usr/lib/tklib0.5" # HACK use amd64 && myconf="${myconf} --enable-64bit" use debug && append-cflags "-DCACHE_REF_DEBUG" - econf ${myconf} || die "configure failed" -} - -src_compile() { - emake || die "emake failed" + econf ${myconf} } src_install() { @@ -70,6 +65,8 @@ src_install() { # subsequently, apps linked against /usr/lib/staden can be run because # loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden' # somehow for gap2caf, for example - echo 'LDPATH=/usr/lib/staden' > 99staden || die + cat >> "${T}"/99staden <<- EOF + LDPATH=/usr/$(get_libdir)/staden + EOF doenvd 99staden } diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild index fa67b6f96..47f7694ab 100644 --- a/sci-biology/staden/staden-9999.ebuild +++ b/sci-biology/staden/staden-9999.ebuild @@ -1,26 +1,24 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=3 -inherit eutils flag-o-matic base subversion # autotools +inherit base eutils flag-o-matic fortran-2 multilib subversion -DESCRIPTION="A fully developed set of DNA sequence assembly (Gap4), editing and analysis tools (Spin)." -HOMEPAGE="http://sourceforge.net/projects/staden" +DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)" +HOMEPAGE="http://sourceforge.net/projects/staden/" # https://staden.svn.sourceforge.net/svnroot/staden staden if [ "$PV" == "9999" ]; then ESVN_REPO_URI="https://staden.svn.sourceforge.net/svnroot/staden/staden/trunk" - #KEYWORDS="~amd64 ~x86" else SRC_URI="http://downloads.sourceforge.net/staden/staden-2.0.0b7-src.tar.gz" - #KEYWORDS="~amd64 ~x86" fi LICENSE="staden" SLOT="0" KEYWORDS="" -IUSE="debug fortran X png curl tcl tk zlib" +IUSE="curl debug fortran png tcl tk X zlib" # either g77 or gfortran must be available # edit src/mk/linux.mk accordingly @@ -28,23 +26,20 @@ IUSE="debug fortran X png curl tcl tk zlib" # # this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058 # -# # -DEPEND="dev-vcs/subversion - >=dev-lang/tk-8.4 - >=dev-lang/tcl-8.4 - dev-tcltk/tklib - >=sci-libs/io_lib-1.12.2 - >=sys-libs/zlib-1.2 - >=media-libs/libpng-1.2 - sci-biology/samtools - >=app-arch/xz-utils-4.999" - -# maybe we should depend on app-arch/lzma or app-arch/xz-utils? - -RDEPEND="tcl? ( >=dev-tcltk/itcl-3.2 ) - tk? ( >=dev-tcltk/itk-3.2 ) - >=dev-tcltk/iwidgets-4.0" +DEPEND=" + app-arch/xz-utils + dev-lang/tk + dev-tcltk/tklib + >=media-libs/libpng-1.2 + sci-biology/samtools + >=sci-libs/io_lib-1.12.2 + >=sys-libs/zlib-1.2 + virtual/fortran" +RDEPEND="${DEPEND} + >=dev-tcltk/iwidgets-4.0 + tcl? ( >=dev-tcltk/itcl-3.2 ) + tk? ( >=dev-tcltk/itk-3.2 )" src_unpack() { if [ "$PV" == "9999" ]; then @@ -67,16 +62,15 @@ src_configure() { use amd64 && myconf="${myconf} --enable-64bit" use debug && append-cflags "-DCACHE_REF_DEBUG" use debug && append-cxxflags "-DCACHE_REF_DEBUG" - econf ${myconf} || die "configure failed" - emake || die "emake failed" -} - -src_compile() { - emake || die "emake failed" + econf ${myconf} } src_install() { emake install DESTDIR="${D}" || die "make install failed" - echo "STADENROOT="${EPREFIX}"/usr/share/staden" > "${S}"/99staden + + cat >> "${S}"/99staden <<- EOF + STADENROOT="${EPREFIX}"/usr/share/staden + EOF + doenvd "${S}"/99staden || die } diff --git a/sci-biology/tablet-bin/Manifest b/sci-biology/tablet-bin/Manifest index f9e28ae52..d47503418 100644 --- a/sci-biology/tablet-bin/Manifest +++ b/sci-biology/tablet-bin/Manifest @@ -1,5 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX response.varfile 645 RMD160 4662694266ac6104b5829923e5b6099ff68552f3 SHA1 971f052ae515bb630d166651adbf06005762b0a0 SHA256 29c9e65e81636b977ec0439f650d83b3cbfc3d23aef600339e4c8949fcd5369f DIST coveragestats.py 4800 RMD160 a45ef0ef293d08c62f79d4921c810554cea5cc44 SHA1 87b2e3432919c8cd2eb673bd8cf4a59f34d4a58e SHA256 358b686d00fd75d2cc9af490b0e7d635f74cbb1c0b153df22d8ff879884d47bc DIST tablet_linux_x86_1_11_05_03.sh 24035425 RMD160 1d36db184cb79b93bd8460e9be293514d7db93d6 SHA1 42580d61f3c725fd357776538484ecc442c2c797 SHA256 3c7de5f0e5d37019485612723dfd3b17fd34e24df8986eb535fcb0335f8b2e99 -EBUILD tablet-bin-1.11.05.03.ebuild 3145 RMD160 6b74a2d66d74893a22380b0bc40853ba2bdb316e SHA1 8bf49eb7bf048d37942c6762125c7ab8ec9ab296 SHA256 fb6bc253d4ad10b5c5ab26f62394e46427b69b37c3f7ec0d03631b1ff372d24b +EBUILD tablet-bin-1.11.05.03.ebuild 3145 RMD160 3b9ac0279bd286fdf48801d5c1e54a028853f770 SHA1 fa826a6f22c1c3e6e2dacd42b538302d4c4a25c3 SHA256 24d671f4f0be32a3989d00b7ef545f6ead12bb1819f90539e833f2bca01c5759 MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EiTQACgkQgAnW8HDreRYRTwCfTWaPyk1yHX+1i3YIkuh7+C38 +NVQAnj2ZKs20U5bdiPnxgg5bQL6tOobe +=aZHh +-----END PGP SIGNATURE----- diff --git a/sci-biology/tablet-bin/tablet-bin-1.11.05.03.ebuild b/sci-biology/tablet-bin/tablet-bin-1.11.05.03.ebuild index 5f066d618..49983e32a 100644 --- a/sci-biology/tablet-bin/tablet-bin-1.11.05.03.ebuild +++ b/sci-biology/tablet-bin/tablet-bin-1.11.05.03.ebuild @@ -4,7 +4,7 @@ EAPI=3 -inherit python java-pkg-2 +inherit java-pkg-2 python DESCRIPTION="Graphical viewer for next generation sequence assemblies and alignments." HOMEPAGE="http://bioinf.scri.ac.uk/tablet/" diff --git a/sci-biology/tclust/ChangeLog b/sci-biology/tclust/ChangeLog new file mode 100644 index 000000000..049bd0800 --- /dev/null +++ b/sci-biology/tclust/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/tclust +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*tclust-110625 (25 Jun 2011) + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -tclust-0.1.ebuild, + +tclust-110625.ebuild, +files/tclust-110625-build.patch: + Cleaned ebuild + diff --git a/sci-biology/tclust/Manifest b/sci-biology/tclust/Manifest index 1298508f3..492f9b251 100644 --- a/sci-biology/tclust/Manifest +++ b/sci-biology/tclust/Manifest @@ -1,4 +1,16 @@ -DIST cdbfasta.tar.gz 59735 RMD160 c90e0ede03a01bf2da77f9beaa3c97fa7e46ff2a SHA1 2419421ab1d753d3bb8778c92236da74fee30526 SHA256 68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c -DIST tclust.tar.gz 9521 RMD160 380e9811be58a2ab9659d25ade0b2a89d705c60f SHA1 42dec7cb63b895730babff5522b257c45001b016 SHA256 d222a7109ec135d5e80767046c47aa6d4201ae779e5d516771b377dbbd261798 -EBUILD tclust-0.1.ebuild 1219 RMD160 f5fb3902935005c2bcf61b12d36fc7bc36b9285a SHA1 305e0d1f49181e7a4ddb95395750e1c8e39fc982 SHA256 d0f33ac7b2b10d1295cd303bca041464849d59174aebb31e9877f964f8d24f97 +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +AUX tclust-110625-build.patch 1292 RMD160 4d97931504dba7b9a1c2d72430b2a63417cc9ea6 SHA1 0db6225234b85cc81fc744b0650e0108eed024f7 SHA256 70134ca266c8903da42b19e432e7b6c1840fe29f8139cf7f8c6e3742a4a43a56 +DIST gclib-110625.tar.gz 82727 RMD160 f12395354b47980577e9d83cc100a6bf6568bd33 SHA1 4c433e6a87663211dc00e2d855a11a058e5b6b48 SHA256 0c7f21fc92b033cd442b672e9014e3ffb9f2de97769ca525715692ed9359439b +DIST tclust-110625.tar.gz 9521 RMD160 380e9811be58a2ab9659d25ade0b2a89d705c60f SHA1 42dec7cb63b895730babff5522b257c45001b016 SHA256 d222a7109ec135d5e80767046c47aa6d4201ae779e5d516771b377dbbd261798 +EBUILD tclust-110625.ebuild 690 RMD160 844b13e2acc2e7aed99b5be134dbe2113077638f SHA1 f2adcfcc2803411baf02dadb0ea9db2f31328851 SHA256 b9fdd5b6e2844165b3d1862ba8a0fdf5cdced5403faacddec7d33c38dcf6ac04 +MISC ChangeLog 293 RMD160 0ef9d9f4df6e14863342c316a3d2911a9bb7d315 SHA1 d777b3cf178b10a4f15b0194fbdbd074e41926b7 SHA256 048c8e8d3667f6d087100b9f84fa0a36f058d60b8e99dc7e7c7d8ca39870ed10 MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F/gMACgkQgAnW8HDreRYIlACfbxspQ6szup9+y0u/154r+iAM +IfkAoIQDAlCRsGAkjROODFzIu0eNtnI3 +=VNJs +-----END PGP SIGNATURE----- diff --git a/sci-biology/tclust/files/tclust-110625-build.patch b/sci-biology/tclust/files/tclust-110625-build.patch new file mode 100644 index 000000000..9474916af --- /dev/null +++ b/sci-biology/tclust/files/tclust-110625-build.patch @@ -0,0 +1,43 @@ + Makefile | 9 ++++----- + 1 files changed, 4 insertions(+), 5 deletions(-) + +diff --git a/Makefile b/Makefile +index f4f69f1..30ba16e 100644 +--- a/Makefile ++++ b/Makefile +@@ -11,8 +11,8 @@ SYSTYPE := $(shell uname) + + # C compiler + +-CC := g++ +-CFLAGS = -O2 -Wall ${SEARCHDIRS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-exceptions -fno-rtti -fno-strict-aliasing ++CC ?= g++ ++CXXFLAGS += -Wall ${SEARCHDIRS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-exceptions -fno-rtti -fno-strict-aliasing + + %.o : %.c + ${CC} ${CFLAGS} -c $< -o $@ +@@ -24,7 +24,7 @@ CFLAGS = -O2 -Wall ${SEARCHDIRS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_ + ${CC} ${CFLAGS} -c $< -o $@ + + %.o : %.cpp +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.cxx + ${CC} ${CFLAGS} -c $< -o $@ +@@ -32,14 +32,13 @@ CFLAGS = -O2 -Wall ${SEARCHDIRS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_ + # C/C++ linker + + LINKER := g++ +-LDFLAGS = + LOADLIBES := + + .PHONY : all + all: tclust + + tclust: ./tclust.o ${GCLDIR}/GBase.o ${GCLDIR}/GStr.o ${GCLDIR}/GArgs.o +- ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} ++ ${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} + + # target for removing all object files + diff --git a/sci-biology/tclust/tclust-0.1.ebuild b/sci-biology/tclust/tclust-0.1.ebuild deleted file mode 100644 index e41de0785..000000000 --- a/sci-biology/tclust/tclust-0.1.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -DESCRIPTION="transitive closure clustering tool with overlap filtering options from TIGR Gene Indices project tools" -HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/" -SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz - ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="${DEPEND}" - -S=${WORKDIR} - -src_prepare() { - # we need gclib from cdbfasta.tar.gz bundle which has fewer files than tgi_cpp_library.tar.gz wbut has e.g. GStr.h - sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' "${S}"/${PN}/Makefile || die "Failed to run sed" - sed -i 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#' "${S}"/"${PN}"/Makefile || die - cd ${PN} || die - ln -s ../cdbfasta/gcl . || die "Cannot make a softlink" -} - -src_compile() { - cd ${PN} || die - emake || die "emake failed in "${S}"/${PN}" -} - -src_install() { - cd ${PN} || die - dobin ${PN} || die "Failed to install ${PN} binary" - newdoc README README.${PN} || die -} diff --git a/sci-biology/tclust/tclust-110625.ebuild b/sci-biology/tclust/tclust-110625.ebuild new file mode 100644 index 000000000..563cdabfb --- /dev/null +++ b/sci-biology/tclust/tclust-110625.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Transitive closure clustering tool with overlap filtering options" +HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/" +SRC_URI=" + ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz -> ${P}.tar.gz + ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/gclib.tar.gz -> gclib-${PV}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +S=${WORKDIR}/${PN} + +src_prepare() { + epatch "${FILESDIR}"/${P}-build.patch + tc-export CC CXX +} + +src_install() { + dobin ${PN} + dodoc README +} diff --git a/sci-biology/tigr-assembler/ChangeLog b/sci-biology/tigr-assembler/ChangeLog index 8ac88cca5..adc4f70cf 100644 --- a/sci-biology/tigr-assembler/ChangeLog +++ b/sci-biology/tigr-assembler/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/tigr-assembler -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> tigr-assembler-2.0.ebuild: + Some ebuild cleaning + 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +tigr-assembler-2.0.ebuild: Mass import from sunrise diff --git a/sci-biology/tigr-assembler/Manifest b/sci-biology/tigr-assembler/Manifest index 826770d5c..0df073a6d 100644 --- a/sci-biology/tigr-assembler/Manifest +++ b/sci-biology/tigr-assembler/Manifest @@ -1,5 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX run_TA 1114 RMD160 a4889d91040e823a8caee8fc2eca6b8a7b38e97c SHA1 b69635740623566bf1658716958cb7a00afb5bbd SHA256 4b3ba31d7308932db000f66dbc4f5b12689efef2a125606ca7336c054770240a DIST TIGR_Assembler_v2.tar.gz 3252950 RMD160 5b7eaeebf8791acb3b53ab864f6e9c6571c70877 SHA1 8bd1886eb33d203598ac03decc7798a1fa0d85d7 SHA256 b5b660db388788173f7bd9778fe9b1e904bed7f6a464ab6cc92cd4608e70fd42 -EBUILD tigr-assembler-2.0.ebuild 1302 RMD160 abb59c33ee5f843f91cbb46cebda010560b7d0c0 SHA1 9b34eb85a125e774b9d772509c8725be7ac1663a SHA256 dd12539261adda1cc0311d036a2acbb4d81c91b9f14b541c2de6917665460b1a -MISC ChangeLog 366 RMD160 456390461b0286ece0f75002dcd49f90bd42e754 SHA1 a6d057fde4a594d8fb2d127bbb443d85ea039d9a SHA256 9b8273b2bfb0bd78ef4656523a6edd6e4fc4d4467c90fdc34995c1f95662c288 -MISC metadata.xml 312 RMD160 ba3ddd549c5d72f3c8872d00fb4c7c3131c5e9f5 SHA1 48b455ee7b2d56564438e66b1d81f72532cf3668 SHA256 02c1f9ac5ad24abc92c3a40e0340c9b2cb8874c00399013d20320141ecb43981 +EBUILD tigr-assembler-2.0.ebuild 1271 RMD160 3af030d6e00632bbd8819795732a2f6fea201df1 SHA1 d7a84e1a500a34b0c40cae5895be2897f7fdca16 SHA256 2953ddfc984238a12248fb19a51b28530f2dd28ff7e08c1d83857e6968968f96 +MISC ChangeLog 464 RMD160 923d85af2185c47f596cfdcb8390efa452d27930 SHA1 078287d84a8545710ac3e1b0022b1c87eff7249f SHA256 ea1e2b2acda2a1de1e3f7448e2a8abe71f4060a0d4590765a457eb1526c4793b +MISC metadata.xml 320 RMD160 4be5330790446398bad0fdababbe2ae8d5369ce3 SHA1 24457ce23ce8facf3852f9c3c35e574b9ee0785e SHA256 338be70c2ea8c0c6f5601311f86117f727fbd96e3b4908784a14683acd7c6601 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EznQACgkQgAnW8HDreRZU7wCfcWTJgYTrEZ33/hUANGkXdJPM +AgIAn3hu50aM69GZMk6OtQuO/cOs7jvS +=tMO2 +-----END PGP SIGNATURE----- diff --git a/sci-biology/tigr-assembler/tigr-assembler-2.0.ebuild b/sci-biology/tigr-assembler/tigr-assembler-2.0.ebuild index 0247b44a0..a55c067ff 100644 --- a/sci-biology/tigr-assembler/tigr-assembler-2.0.ebuild +++ b/sci-biology/tigr-assembler/tigr-assembler-2.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -13,9 +13,6 @@ SLOT="0" IUSE="" KEYWORDS="~amd64 ~x86" -DEPEND="" -RDEPEND="${DEPEND}" - S="${WORKDIR}/TIGR_Assembler_v2" src_prepare() { diff --git a/sci-biology/tigr-foundation-libs/ChangeLog b/sci-biology/tigr-foundation-libs/ChangeLog new file mode 100644 index 000000000..583614555 --- /dev/null +++ b/sci-biology/tigr-foundation-libs/ChangeLog @@ -0,0 +1,8 @@ +# ChangeLog for sci-biology/tigr-foundation-libs +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> + tigr-foundation-libs-2.0-r1.ebuild: + Some ebuild cleaning + diff --git a/sci-biology/tigr-foundation-libs/Manifest b/sci-biology/tigr-foundation-libs/Manifest index 92f8cbbad..3e0ae1f33 100644 --- a/sci-biology/tigr-foundation-libs/Manifest +++ b/sci-biology/tigr-foundation-libs/Manifest @@ -1,4 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX TigrFoundation-all-patches.patch 2071 RMD160 ce194684d054613b254fa5f41fd31e520fe1cf5b SHA1 4a3f0d061b8024abb21178feeef3b1256e4117ac SHA256 e13f6136ef336e54ecc24d0e34e65e1ab827cfb7365b2d2686541ceed3cd6ac5 DIST autoEditor-1.20.tar.gz 2438903 RMD160 598ac977eb424959fc052b4c857ef4487b7e13f9 SHA1 985b5e880148a904b157295053945f9530718d30 SHA256 c0c399eda52a10deb0e0362b4caf909014768a4d08e90c900392cdf712cefd66 -EBUILD tigr-foundation-libs-2.0-r1.ebuild 901 RMD160 21432c20a478821460f5023f3f04d790656d0478 SHA1 79628e3286811af4cd3e97899ee77430f7c1a642 SHA256 5ceb776c2c45b9e105e6d0382be97f5a4e070504c1af674a2c0737e36552f7e8 -MISC metadata.xml 261 RMD160 ce19afc5fdd536a9eadb35a705f09613e3774e32 SHA1 b95b491e808c8dd5a106edae7e48af4f8d61f58a SHA256 e3766426d46af16432093cd9fb8a2df3862c77ef313ad175ca2ef60af5cee6f5 +EBUILD tigr-foundation-libs-2.0-r1.ebuild 870 RMD160 330a00f7479fc33127ad2843045e47c35b09cdcf SHA1 533dc4ae3a82c2b9f8727f4acde9b5d41ffcdf1b SHA256 674553bbc205a83b2070a8cca1806bf44e50a687ea6e67d0c799b210f87fa0a3 +MISC ChangeLog 242 RMD160 fbaa9a69394a8f13e55c33a03460f547d35ff58f SHA1 597023def99a74e8772d980836a88a320392cc8a SHA256 e4d3c69604699333eec2b02fe46afe50432f3ee17104612adff3c4a99f912c7d +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4EzqAACgkQgAnW8HDreRavZwCeJHLxV+A4K3Q5mFy2qjBnn5cA +p9gAnio/NdUn1JiPJuhmi2iL4sQrqcfi +=DrAT +-----END PGP SIGNATURE----- diff --git a/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild b/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild index 18df09e4b..61068e4d5 100644 --- a/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild +++ b/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -18,9 +18,6 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND="" -RDEPEND="${DEPEND}" - S="${WORKDIR}"/autoEditor-1.20/TigrFoundation-2.0 src_prepare(){ diff --git a/sci-biology/wcd/ChangeLog b/sci-biology/wcd/ChangeLog new file mode 100644 index 000000000..19bb05dc9 --- /dev/null +++ b/sci-biology/wcd/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/wcd +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*wcd-0.6.0 (25 Jun 2011) + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -wcd-0.6.0_beta.ebuild, + +wcd-0.6.0.ebuild: + Cleaned ebuild + diff --git a/sci-biology/wcd/Manifest b/sci-biology/wcd/Manifest index 8f7fc7749..4fc1c885b 100644 --- a/sci-biology/wcd/Manifest +++ b/sci-biology/wcd/Manifest @@ -1,3 +1,14 @@ -DIST wcd-0.6.0B.tar.gz 595214 RMD160 eda5edf8215f0b723c5d1e970f36cb3e97b09e6f SHA1 988f944d4a6cd0894a864fa990f0f6eaab3b94bd SHA256 58a02677a0d89f9c2ff89f6f0ef9f5ce9caa487ff3f85a0a73fb9da0ec138509 -EBUILD wcd-0.6.0_beta.ebuild 1071 RMD160 ed692f6030456ff3f05c74e949c5e638ede04f64 SHA1 4d49e12d08a438222df4a6333c040ec614abb32e SHA256 3b84ec384dd12ecb97372b8959703375a422a4a4959af9a954769c3b18bef3ff -MISC metadata.xml 261 RMD160 ce19afc5fdd536a9eadb35a705f09613e3774e32 SHA1 b95b491e808c8dd5a106edae7e48af4f8d61f58a SHA256 e3766426d46af16432093cd9fb8a2df3862c77ef313ad175ca2ef60af5cee6f5 +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +DIST wcd-0.6.0.tar.gz 595214 RMD160 eda5edf8215f0b723c5d1e970f36cb3e97b09e6f SHA1 988f944d4a6cd0894a864fa990f0f6eaab3b94bd SHA256 58a02677a0d89f9c2ff89f6f0ef9f5ce9caa487ff3f85a0a73fb9da0ec138509 +EBUILD wcd-0.6.0.ebuild 973 RMD160 3d00bc12ea340547f4fdf0a89eb2f1fb31392747 SHA1 28958b7829c5cc0235e0466586ffe46f9fdc5bb8 SHA256 23e8405f1cc13e1757e9d2dc6c977d0aa49f8b3f289e74cc2742cd5eb08b3f3d +MISC ChangeLog 252 RMD160 81599f287c3039cbe19f123d6d1d84497d64069f SHA1 49342a48f0625cbd073ef422c4b3c9ad8023b6e7 SHA256 66b8f77a881dfaacbd55af73ff2babfcd98df06c82271233b08adadc9cdb01e3 +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F8ewACgkQgAnW8HDreRbOIgCgszlZYbNNJke5eKkilI0GC4eQ +s4gAoMes0BTxyr3lJKNv7FVO3MGwKR5Q +=dC9T +-----END PGP SIGNATURE----- diff --git a/sci-biology/wcd/wcd-0.6.0.ebuild b/sci-biology/wcd/wcd-0.6.0.ebuild new file mode 100644 index 000000000..3367cc404 --- /dev/null +++ b/sci-biology/wcd/wcd-0.6.0.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 + +inherit eutils flag-o-matic + +DESCRIPTION="Sequence clustering by either of: d2 function, edit distance, common word heuristics" +HOMEPAGE="http://code.google.com/p/wcdest/" +SRC_URI="http://wcdest.googlecode.com/files/${P}B.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="doc mpi threads" + +DEPEND="mpi? ( sys-cluster/mpich2 )" +RDEPEND="" + +S="${WORKDIR}"/wcd-0.6.0 + +src_configure(){ + local myconf="" + if use mpi; then + myconf="${myconf} --enable-mpi" + fi + + if use threads; then + myconf="${myconf} --enable-pthreads" + fi + + econf ${myconf} +} + +src_compile() { + emake + if use doc; then + emake pdf info html + fi +} + +src_install() { + local f + emake PREFIX=/usr DESTDIR="${D}" LIBDIR="${D}"usr/$(get_libdir) install + + if use doc; then + for f in README doc/wcd.html doc/wcd.pdf doc/wcd.texi; do + dodoc ${f} + done + fi +} diff --git a/sci-biology/wcd/wcd-0.6.0_beta.ebuild b/sci-biology/wcd/wcd-0.6.0_beta.ebuild deleted file mode 100644 index f7fbd7558..000000000 --- a/sci-biology/wcd/wcd-0.6.0_beta.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit flag-o-matic eutils - -DESCRIPTION="wcd clusters sequences (typically ESTs) by either of: d2 function, edit distance, common word heuristics." -HOMEPAGE="http://code.google.com/p/wcdest" -SRC_URI="http://wcdest.googlecode.com/files/wcd-0.6.0B.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~x86 ~amd64" -IUSE="mpi threads" - -DEPEND="mpi? ( sys-cluster/mpich2 )" -RDEPEND="" - -S="${WORKDIR}"/wcd-0.6.0 - -src_prepare(){ - mv "${DESTDIR}"/wcd-0.6.0B.tar.gz "${DESTDIR}"/wcd-0.6.0.tar.gz || die -} - -src_compile(){ - local myconf="" - if use mpi; then - myconf="${myconf} --enable-mpi" - fi - - if use threads; then - myconf="${myconf} --enable-pthreads" - fi - - econf ${myconf} || die - - emake || die - emake pdf || die - emake info || die - emake html || die -} - -src_install() { - emake PREFIX=/usr DESTDIR="${D}" LIBDIR="${D}"usr/$(get_libdir) install \ - || die "make install failed" - for f in README doc/wcd.html doc/wcd.pdf doc/wcd.texi; do dodoc ${f} || die; done -} diff --git a/sci-biology/zmsort/ChangeLog b/sci-biology/zmsort/ChangeLog new file mode 100644 index 000000000..7e45e0a2c --- /dev/null +++ b/sci-biology/zmsort/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/zmsort +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*zmsort-110625 (25 Jun 2011) + + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -zmsort-0.1.ebuild, + +zmsort-110625.ebuild, +files/zmsort-110625-build.patch: + Cleaned ebuild + diff --git a/sci-biology/zmsort/Manifest b/sci-biology/zmsort/Manifest index 52cdae403..6fa0e1f31 100644 --- a/sci-biology/zmsort/Manifest +++ b/sci-biology/zmsort/Manifest @@ -1,4 +1,16 @@ -DIST cdbfasta.tar.gz 59735 RMD160 c90e0ede03a01bf2da77f9beaa3c97fa7e46ff2a SHA1 2419421ab1d753d3bb8778c92236da74fee30526 SHA256 68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c -DIST zmsort.tar.gz 6192 RMD160 ccd1996ac194ee9b34044f585b3a82b94e07b7d5 SHA1 d0f0adca786f33329c5be93740ba9910c09c64d6 SHA256 8267592ec5ddb070a5feb07fcf475ce13ec28cdda33d685a218098bd6bc2962f -EBUILD zmsort-0.1.ebuild 1310 RMD160 f59ce932feb35dcc054fe86ce8c66b768967e1d5 SHA1 d5e6a043d362d22dfb2dea3c1c5e2bb2ae2c4dd3 SHA256 ce2fd5d34bc8a39285ce71308b646b469491b9efcf79404be0f2d18d6561ef47 +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +AUX zmsort-110625-build.patch 1188 RMD160 c9cafc93f2b64a47f29ae0b847913fe829973dfb SHA1 020f892aae2090f7149f7566d9b3b9cd45167b22 SHA256 6d5a8fb86bba20b92a526dcf7f9db893668e21f569fe6af78c5cfc8b9bf66b7e +DIST gclib-110625.tar.gz 82727 RMD160 f12395354b47980577e9d83cc100a6bf6568bd33 SHA1 4c433e6a87663211dc00e2d855a11a058e5b6b48 SHA256 0c7f21fc92b033cd442b672e9014e3ffb9f2de97769ca525715692ed9359439b +DIST zmsort-110625.tar.gz 6192 RMD160 ccd1996ac194ee9b34044f585b3a82b94e07b7d5 SHA1 d0f0adca786f33329c5be93740ba9910c09c64d6 SHA256 8267592ec5ddb070a5feb07fcf475ce13ec28cdda33d685a218098bd6bc2962f +EBUILD zmsort-110625.ebuild 698 RMD160 d4a6036541b04b17060b105830ff229d6379cf31 SHA1 3e5166d7afc2fd12ba880e71273fda39194aed32 SHA256 3393c1030128e87fefec376411923748c18698c641381b232c1e2e6e6d454c31 +MISC ChangeLog 293 RMD160 f961b1d43e475cd93fd62c98be34521770d284c7 SHA1 5dfbee5d688c55dc9a58f6359e83420d4e86db16 SHA256 c62d31ed38b317b278a9d026cd5eb78fb154418c1327893ee970e005d81ea84a MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEAREIAAYFAk4F/tcACgkQgAnW8HDreRaDzgCgtvLzI/SDlJtObDEWHN5L+h2j +kAAAoKTXfitPox+bygIBTnazLcOfr0+S +=OOC7 +-----END PGP SIGNATURE----- diff --git a/sci-biology/zmsort/files/zmsort-110625-build.patch b/sci-biology/zmsort/files/zmsort-110625-build.patch new file mode 100644 index 000000000..3c6fe8a40 --- /dev/null +++ b/sci-biology/zmsort/files/zmsort-110625-build.patch @@ -0,0 +1,41 @@ + Makefile | 7 +++---- + 1 files changed, 3 insertions(+), 4 deletions(-) + +diff --git a/Makefile b/Makefile +index 82e16a0..f9505e0 100644 +--- a/Makefile ++++ b/Makefile +@@ -12,7 +12,7 @@ SYSTYPE := $(shell uname) + # C compiler + + CC := g++ +-CFLAGS = -O2 -Wall ${SEARCHDIRS} -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 \ ++CXXFLAGS += -Wall ${SEARCHDIRS} -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 \ + -fno-exceptions -fno-rtti -fno-strict-aliasing -D_REENTRANT + + %.o : %.c +@@ -25,7 +25,7 @@ CFLAGS = -O2 -Wall ${SEARCHDIRS} -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 \ + ${CC} ${CFLAGS} -c $< -o $@ + + %.o : %.cpp +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.cxx + ${CC} ${CFLAGS} -c $< -o $@ +@@ -33,14 +33,13 @@ CFLAGS = -O2 -Wall ${SEARCHDIRS} -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 \ + # C/C++ linker + + LINKER := g++ +-LDFLAGS = + LOADLIBES := + + .PHONY : all + all: zmsort + + zmsort: ./zmsort.o ${GCLDIR}/GBase.o ${GCLDIR}/GStr.o ${GCLDIR}/GArgs.o +- ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} ++ ${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} + + # target for removing all object files + diff --git a/sci-biology/zmsort/zmsort-0.1.ebuild b/sci-biology/zmsort/zmsort-0.1.ebuild deleted file mode 100644 index 2cec398e8..000000000 --- a/sci-biology/zmsort/zmsort-0.1.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -DESCRIPTION="merge-sort utility for compressed alignment files, with multi-file output option from TIGR Gene Indices project tools" -HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/" -SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz - ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="${DEPEND}" - -S=${WORKDIR} - -src_prepare() { - # we need gclib from cdbfasta.tar.gz bundle which has fewer files than tgi_cpp_library.tar.gz wbut has e.g. GStr.h - sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' "${S}"/${PN}/Makefile || die "Failed to run sed" - sed -i 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#' "${S}"/"${PN}"/Makefile || die - sed -i 's/-V\t\tverbose/-V\t\tverbose\\/' "${S}"/"${PN}"/zmsort.cpp || die - cd ${PN} || die - ln -s ../cdbfasta/gcl . || die "Cannot make a softlink" -} - -src_compile() { - cd ${PN} || die - emake || die "emake failed in "${S}"/${PN}" -} - -src_install() { - cd ${PN} || die - dobin ${PN} || die "Failed to install ${PN} binary" - newdoc README README.${PN} || die -} diff --git a/sci-biology/zmsort/zmsort-110625.ebuild b/sci-biology/zmsort/zmsort-110625.ebuild new file mode 100644 index 000000000..7d2920411 --- /dev/null +++ b/sci-biology/zmsort/zmsort-110625.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Merge-sort utility for compressed alignment files, with multi-file output" +HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/" +SRC_URI=" + ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz -> ${P}.tar.gz + ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/gclib.tar.gz -> gclib-${PV}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +S=${WORKDIR}/${PN} + +src_prepare() { + epatch "${FILESDIR}"/${P}-build.patch + tc-export CC CXX +} + +src_install() { + dobin ${PN} + dodoc README +} |