diff options
Diffstat (limited to 'sci-biology')
100 files changed, 0 insertions, 1599 deletions
diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog deleted file mode 100644 index 2ae77445a..000000000 --- a/sci-biology/amos/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/amos -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> ChangeLog: - Mass import from sunrise - - 20 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> amos-2.0.2.ebuild: - fix die messages - - 20 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +amos-2.0.2.ebuild, +metadata.xml: - new package (bug 175293) - diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest deleted file mode 100644 index 797538554..000000000 --- a/sci-biology/amos/Manifest +++ /dev/null @@ -1,16 +0,0 @@ -DIST amos-2.0.2.tar.gz 1822049 RMD160 6cf5f6afbc98494a9799fce678cab7f24a5c9d0d SHA1 de49a1f89b0a4ee994add23bdabe5841bcff6d68 SHA256 1bffa59ffe35a26f8328d49ac94df9f0f1be0c324954fd53f041c63353272416 -EBUILD amos-2.0.2.ebuild 605 RMD160 c2a5f45a542647d5460f5aa52eae46a9e44e7cc6 SHA1 bc2294caaacfba02e012d76ee1971fb5344ce4b9 SHA256 fa2320d424535504edd64a82be5bd9104ec981b1ec6e051de4c21d3f5ac8d8ae -MD5 64b90f8c844d0a9d74ab402cfedb09fb amos-2.0.2.ebuild 605 -RMD160 c2a5f45a542647d5460f5aa52eae46a9e44e7cc6 amos-2.0.2.ebuild 605 -SHA256 fa2320d424535504edd64a82be5bd9104ec981b1ec6e051de4c21d3f5ac8d8ae amos-2.0.2.ebuild 605 -MISC ChangeLog 420 RMD160 21fed08e83092846b647b550c24b9ff5e0827b9a SHA1 0e1129d82c9b41196c5446f30950b99b07c08b91 SHA256 a8825ccc7fb112030924858a10106305ee797c008ef9751846264316f2479838 -MD5 ffa1f8cc6f2d4feb2368c70c1819f058 ChangeLog 420 -RMD160 21fed08e83092846b647b550c24b9ff5e0827b9a ChangeLog 420 -SHA256 a8825ccc7fb112030924858a10106305ee797c008ef9751846264316f2479838 ChangeLog 420 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 -MD5 1e678929a9fec6632e227bdf2262e9a1 metadata.xml 170 -RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 metadata.xml 170 -SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 metadata.xml 170 -MD5 228b8e9fef24c934d9d6873b879b55f2 files/digest-amos-2.0.2 235 -RMD160 a525ec025623d938b6aac7a445b29b25c9312c39 files/digest-amos-2.0.2 235 -SHA256 c33383fe3ec9a19443247a6e33946b1aafbe6c8484ba1bd27443bb0db2076b97 files/digest-amos-2.0.2 235 diff --git a/sci-biology/amos/amos-2.0.2.ebuild b/sci-biology/amos/amos-2.0.2.ebuild deleted file mode 100644 index 23584bbc0..000000000 --- a/sci-biology/amos/amos-2.0.2.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit qt3 - -DESCRIPTION="A Modular, Open-Source whole genome assembler" -HOMEPAGE="http://amos.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -IUSE="" -KEYWORDS="~x86" - -DEPEND="$(qt_min_version 3.3)" -RDEPEND="${DEPEND} - sci-biology/mummer" - -src_compile() { - econf || die "econf failed" - # TODO: fix parallel make. Notified upstream - emake -j1 || die "emake failed" -} - -src_install() { - emake DESTDIR="${D}" install || die "install failed" -} diff --git a/sci-biology/amos/files/digest-amos-2.0.2 b/sci-biology/amos/files/digest-amos-2.0.2 deleted file mode 100644 index 2584a1b6b..000000000 --- a/sci-biology/amos/files/digest-amos-2.0.2 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 ea4182c2647bbab1ee38e59e5383786b amos-2.0.2.tar.gz 1822049 -RMD160 6cf5f6afbc98494a9799fce678cab7f24a5c9d0d amos-2.0.2.tar.gz 1822049 -SHA256 1bffa59ffe35a26f8328d49ac94df9f0f1be0c324954fd53f041c63353272416 amos-2.0.2.tar.gz 1822049 diff --git a/sci-biology/amos/metadata.xml b/sci-biology/amos/metadata.xml deleted file mode 100644 index 7e3286984..000000000 --- a/sci-biology/amos/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>maintainer-wanted</herd> -</pkgmetadata> diff --git a/sci-biology/blat/ChangeLog b/sci-biology/blat/ChangeLog deleted file mode 100644 index 2b7ceafad..000000000 --- a/sci-biology/blat/ChangeLog +++ /dev/null @@ -1,17 +0,0 @@ -# ChangeLog for sci-biology/blat -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 30 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +blat-34.ebuild: - version bump! - - 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +blat-33.ebuild: - Mass import from sunrise - - 05 Oct 2006; Markus Ullmann <jokey@gentoo.org> blat-33.ebuild: - Small QA - - 25 Sep 2006; Andrey Kislyuk (weaver) <weaver@horizon.ath.cx> +blat-33.ebuild, - +metadata.xml: - new ebuild: sci-biology/blat-33 (bug 135307) - diff --git a/sci-biology/blat/Manifest b/sci-biology/blat/Manifest deleted file mode 100644 index 5d4c07ec1..000000000 --- a/sci-biology/blat/Manifest +++ /dev/null @@ -1,24 +0,0 @@ -DIST blatSrc33.zip 1308517 RMD160 76d7f8f713a5ece72c63eb8852662acf83e2e736 SHA1 a9606455549e2f153ab04321d08e59f60c039dd2 SHA256 4ca932721f529d815e64b51940c94d8136faec52c6b8bf8c3fcd3706337d9a29 -DIST blatSrc34.zip 2142975 RMD160 6c8226305c56ea56504103db6ef401841bc0c6f7 SHA1 4208451b5fa5f6cf30d15afb1df79edc850735db SHA256 b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629 -EBUILD blat-33.ebuild 812 RMD160 bcc1c8d50d708410dcc1e9bfd650523806209d6b SHA1 851fb369c0d328c3c1add9b94c66aae24fa66bfa SHA256 c80f630e4df9309dbfc599247a04128605a635cccec1c5ec2bf6b02d0f998b2e -MD5 6ce5dcd42aa0c271b0e14f6f1d93cd9d blat-33.ebuild 812 -RMD160 bcc1c8d50d708410dcc1e9bfd650523806209d6b blat-33.ebuild 812 -SHA256 c80f630e4df9309dbfc599247a04128605a635cccec1c5ec2bf6b02d0f998b2e blat-33.ebuild 812 -EBUILD blat-34.ebuild 887 RMD160 acd8641037ab23c784c54bacf4a8e7213953040d SHA1 e152207366ca8608b75a3c5f921e786938f80576 SHA256 918f6fbc8a6ec60f2eee0c07c0581d0826b02795492f72145bbfab3b0815096e -MD5 99214efbec958a7df16f4281f94d9e46 blat-34.ebuild 887 -RMD160 acd8641037ab23c784c54bacf4a8e7213953040d blat-34.ebuild 887 -SHA256 918f6fbc8a6ec60f2eee0c07c0581d0826b02795492f72145bbfab3b0815096e blat-34.ebuild 887 -MISC ChangeLog 526 RMD160 b9715fd25f0863a81b969d7624d67ca6dfc42ab6 SHA1 632cefe41a3dd212aa6debb7e87d93e2b2123417 SHA256 d562514892d95708dd06ee82f0150ffd124dd1540e423a94ad9bd0897867740a -MD5 1f9db8bfc74d836232ee3be23bb3c6ea ChangeLog 526 -RMD160 b9715fd25f0863a81b969d7624d67ca6dfc42ab6 ChangeLog 526 -SHA256 d562514892d95708dd06ee82f0150ffd124dd1540e423a94ad9bd0897867740a ChangeLog 526 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 -MD5 1e678929a9fec6632e227bdf2262e9a1 metadata.xml 170 -RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 metadata.xml 170 -SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 metadata.xml 170 -MD5 762700fd66583fb30a2036fddc991c09 files/digest-blat-33 223 -RMD160 2a3f5a14978a209ed44542f37026dea617d025f7 files/digest-blat-33 223 -SHA256 37fda0a57d5990b4467a5d0ff43a26e8b7e4a0a7dca3ccfe4d0138cd69618b32 files/digest-blat-33 223 -MD5 81ab8b9934a53205396930264fcf07a6 files/digest-blat-34 223 -RMD160 7ac40e4fb8e6fcc9860c4f946868e827bc6f291d files/digest-blat-34 223 -SHA256 86fd983cb6150976e0c6b5eccdce7d0f2c23a97ded547e12a69aa32250d58e33 files/digest-blat-34 223 diff --git a/sci-biology/blat/blat-33.ebuild b/sci-biology/blat/blat-33.ebuild deleted file mode 100644 index 2c694aff1..000000000 --- a/sci-biology/blat/blat-33.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit toolchain-funcs - -DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner" -LICENSE="blat" -HOMEPAGE="http://www.cse.ucsc.edu/~kent/" -SLOT="0" -IUSE="" -KEYWORDS="~x86" - -SRC_URI="http://www.soe.ucsc.edu/~kent/src/${PN}Src${PV}.zip" -S="${WORKDIR}/${PN}Src" - -DEPEND="app-arch/unzip" -RDEPEND="" - -src_compile() { - MACHTYPE=$(tc-arch) - if [[ $MACHTYPE == "x86" ]]; then MACHTYPE="i386"; fi - sed -i 's/-Werror//; s/CFLAGS=//;' "${S}/inc/common.mk" - mkdir -p "${S}/bin/${MACHTYPE}" - emake MACHTYPE="${MACHTYPE}" HOME="${S}" || die "emake failed" -} - -src_install() { - MACHTYPE=$(tc-arch) - if [[ $MACHTYPE == "x86" ]]; then MACHTYPE="i386"; fi - dobin "${S}/bin/${MACHTYPE}/"* -} diff --git a/sci-biology/blat/blat-34.ebuild b/sci-biology/blat/blat-34.ebuild deleted file mode 100644 index 665fdf9fe..000000000 --- a/sci-biology/blat/blat-34.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit toolchain-funcs - -DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner" -LICENSE="blat" -HOMEPAGE="http://www.cse.ucsc.edu/~kent/" -SLOT="0" -IUSE="" -KEYWORDS="~x86" - -SRC_URI="http://www.soe.ucsc.edu/~kent/src/${PN}Src${PV}.zip" -S="${WORKDIR}/${PN}Src" - -DEPEND="app-arch/unzip" -RDEPEND="" - -src_compile() { - MACHTYPE=$(tc-arch) - if [[ $MACHTYPE == "x86" ]]; then MACHTYPE="i386"; fi - sed -i 's/-Werror//; s/CFLAGS=//;' "${S}/inc/common.mk" - sed -i 's/\(${STRIP} \)/#\1/' "${S}"/{*/makefile,utils/*/makefile,*/*.mk} - mkdir -p "${S}/bin/${MACHTYPE}" - emake MACHTYPE="${MACHTYPE}" HOME="${S}" || die "emake failed" -} - -src_install() { - MACHTYPE=$(tc-arch) - if [[ $MACHTYPE == "x86" ]]; then MACHTYPE="i386"; fi - dobin "${S}/bin/${MACHTYPE}/"* -} diff --git a/sci-biology/blat/files/digest-blat-33 b/sci-biology/blat/files/digest-blat-33 deleted file mode 100644 index c1fe634d4..000000000 --- a/sci-biology/blat/files/digest-blat-33 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 5f9d3a4a88e57dfc435b5dd465209918 blatSrc33.zip 1308517 -RMD160 76d7f8f713a5ece72c63eb8852662acf83e2e736 blatSrc33.zip 1308517 -SHA256 4ca932721f529d815e64b51940c94d8136faec52c6b8bf8c3fcd3706337d9a29 blatSrc33.zip 1308517 diff --git a/sci-biology/blat/files/digest-blat-34 b/sci-biology/blat/files/digest-blat-34 deleted file mode 100644 index 18742d057..000000000 --- a/sci-biology/blat/files/digest-blat-34 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 c8637145ea70acf1ced1a670d37d7b98 blatSrc34.zip 2142975 -RMD160 6c8226305c56ea56504103db6ef401841bc0c6f7 blatSrc34.zip 2142975 -SHA256 b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629 blatSrc34.zip 2142975 diff --git a/sci-biology/blat/metadata.xml b/sci-biology/blat/metadata.xml deleted file mode 100644 index 7e3286984..000000000 --- a/sci-biology/blat/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>maintainer-wanted</herd> -</pkgmetadata> diff --git a/sci-biology/blossoc/ChangeLog b/sci-biology/blossoc/ChangeLog deleted file mode 100644 index 00ebd7d0b..000000000 --- a/sci-biology/blossoc/ChangeLog +++ /dev/null @@ -1,11 +0,0 @@ -# ChangeLog for sci-biology/blossoc -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +blossoc-1.1.1.ebuild: - Mass import from sunrise - - 15 Mar 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +blossoc-1.1.1.ebuild, - +metadata.xml: - new package (bug 161063) - diff --git a/sci-biology/blossoc/Manifest b/sci-biology/blossoc/Manifest deleted file mode 100644 index 497e46519..000000000 --- a/sci-biology/blossoc/Manifest +++ /dev/null @@ -1,16 +0,0 @@ -DIST blossoc-1.1.1.tar.gz 615190 RMD160 7c867e69671354abc5affb80d5e879f8fd5c762a SHA1 f71b903b4ffc1dbe832cd19cf0c09da30222b285 SHA256 964ba436d55caa7bf64ba417d43ddd123589494648360074237df195c6fb2dd4 -EBUILD blossoc-1.1.1.ebuild 480 RMD160 b072f0dc8e79d87f2829b56f93cab3ed0026d0c5 SHA1 9e14db25306b54fbd08cac2c518baf32941cf1d4 SHA256 6615272b267a2b9a2ac519cd03e585659631b178d103674e4bd2f356b9dfafd0 -MD5 eafa3d0a2aba386a21b056f18e49502e blossoc-1.1.1.ebuild 480 -RMD160 b072f0dc8e79d87f2829b56f93cab3ed0026d0c5 blossoc-1.1.1.ebuild 480 -SHA256 6615272b267a2b9a2ac519cd03e585659631b178d103674e4bd2f356b9dfafd0 blossoc-1.1.1.ebuild 480 -MISC ChangeLog 347 RMD160 43d9906fdb776920242d4975222a4c7bcccfc8bf SHA1 a2249d6182411f7b7de8edf46d116d7394a723cb SHA256 a8da1493f4ce8884496710c596945fdf3510dc1f098a4ef53a87c96247c198d0 -MD5 101136b031c34531cc89fb4d28bf5d77 ChangeLog 347 -RMD160 43d9906fdb776920242d4975222a4c7bcccfc8bf ChangeLog 347 -SHA256 a8da1493f4ce8884496710c596945fdf3510dc1f098a4ef53a87c96247c198d0 ChangeLog 347 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 -MD5 1e678929a9fec6632e227bdf2262e9a1 metadata.xml 170 -RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 metadata.xml 170 -SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 metadata.xml 170 -MD5 2eab4b45781017a0de6f327c6d137579 files/digest-blossoc-1.1.1 241 -RMD160 f21bd00d39a00d454f439b896733993d5753b09c files/digest-blossoc-1.1.1 241 -SHA256 b515a0a46908b185c870bd4fec981443534bcce5481d512ca6c61f1e1ea12882 files/digest-blossoc-1.1.1 241 diff --git a/sci-biology/blossoc/blossoc-1.1.1.ebuild b/sci-biology/blossoc/blossoc-1.1.1.ebuild deleted file mode 100644 index 38c712866..000000000 --- a/sci-biology/blossoc/blossoc-1.1.1.ebuild +++ /dev/null @@ -1,19 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -DESCRIPTION="A linkage disequilibrium association mapping tool" -HOMEPAGE="http://www.daimi.au.dk/~mailund/Blossoc/" -SRC_URI="http://www.daimi.au.dk/~mailund/Blossoc/download/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -IUSE="" -KEYWORDS="~x86" - -DEPEND="sci-libs/gsl" -RDEPEND="${DEPEND}" - -src_install() { - emake install DESTDIR="${D}" || die "emake install failed" -} diff --git a/sci-biology/blossoc/files/digest-blossoc-1.1.1 b/sci-biology/blossoc/files/digest-blossoc-1.1.1 deleted file mode 100644 index 8b7a8a112..000000000 --- a/sci-biology/blossoc/files/digest-blossoc-1.1.1 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 285394ff3e4c07505266354d4a0887b7 blossoc-1.1.1.tar.gz 615190 -RMD160 7c867e69671354abc5affb80d5e879f8fd5c762a blossoc-1.1.1.tar.gz 615190 -SHA256 964ba436d55caa7bf64ba417d43ddd123589494648360074237df195c6fb2dd4 blossoc-1.1.1.tar.gz 615190 diff --git a/sci-biology/blossoc/metadata.xml b/sci-biology/blossoc/metadata.xml deleted file mode 100644 index 7e3286984..000000000 --- a/sci-biology/blossoc/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>maintainer-wanted</herd> -</pkgmetadata> diff --git a/sci-biology/clover/ChangeLog b/sci-biology/clover/ChangeLog deleted file mode 100644 index f21e33a49..000000000 --- a/sci-biology/clover/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/clover -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> - +clover-2006.07.17.ebuild: - Mass import from sunrise - - 15 Mar 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +clover-2006.07.17.ebuild, - +metadata.xml: - new package (bug 142269) - diff --git a/sci-biology/clover/Manifest b/sci-biology/clover/Manifest deleted file mode 100644 index d0dd1e5f7..000000000 --- a/sci-biology/clover/Manifest +++ /dev/null @@ -1,17 +0,0 @@ -DIST clover-2006-07-17.tar.gz 15610 RMD160 e7f5c2b53afef2df292f9274b2a1ce2c1fbbc0c3 SHA1 f80b528ceb9833d0465b1196ae793c5364a87109 SHA256 e7b5b9fa8a341d49d9cf79a6d03ef0677a493f0c34a9a2f466a864575af91cb9 -DIST jaspar2005core 14913 RMD160 6fe43472cc1a2e0389ad9290801db56488773d3e SHA1 be8cdff62cf35f430c0c17f53564529b08000c9c SHA256 498a560c67411789106b50ccdfd9bc41f571d77c2fe9bfba7e95128c0a122fe4 -EBUILD clover-2006.07.17.ebuild 1059 RMD160 968519d9c6c17d29102ae9b6465acfe3812bcae7 SHA1 873e0f380eac7567ef3c2f9ee29fbc619a31fc4f SHA256 0ed8a75004280210ccd56dfb5c510bca400ece76cddbe3728ea3674f52387bd6 -MD5 1509c4396358a7c57ced969757f1eb1e clover-2006.07.17.ebuild 1059 -RMD160 968519d9c6c17d29102ae9b6465acfe3812bcae7 clover-2006.07.17.ebuild 1059 -SHA256 0ed8a75004280210ccd56dfb5c510bca400ece76cddbe3728ea3674f52387bd6 clover-2006.07.17.ebuild 1059 -MISC ChangeLog 356 RMD160 648c4b8a14af9917a83ef1bcbd8dff38ba42b957 SHA1 c9bde15410e08f200396143117e4ccd3becf7fe9 SHA256 41819363e8b5dcf8d67293fe33b7bd9c91f85acf983e1983b8b70f78a3d39bba -MD5 5d9971961a5b761a9824671bde7ced3d ChangeLog 356 -RMD160 648c4b8a14af9917a83ef1bcbd8dff38ba42b957 ChangeLog 356 -SHA256 41819363e8b5dcf8d67293fe33b7bd9c91f85acf983e1983b8b70f78a3d39bba ChangeLog 356 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 -MD5 1e678929a9fec6632e227bdf2262e9a1 metadata.xml 170 -RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 metadata.xml 170 -SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 metadata.xml 170 -MD5 2fd761a79ad477d120b354d1a5a9baab files/digest-clover-2006.07.17 470 -RMD160 19c7bb7d36860924f2b707673290c6dd8e2d7a3a files/digest-clover-2006.07.17 470 -SHA256 d95bafedeabe12831000becf898ee985b95ff83e269e3d5ee39506fe1287a0d4 files/digest-clover-2006.07.17 470 diff --git a/sci-biology/clover/clover-2006.07.17.ebuild b/sci-biology/clover/clover-2006.07.17.ebuild deleted file mode 100644 index 4cf143b0f..000000000 --- a/sci-biology/clover/clover-2006.07.17.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit versionator toolchain-funcs - -MY_PV=$(replace_all_version_separators '-') - -DESCRIPTION="Cis-eLement OVERrepresentation: Detection of functional DNA motifs" -HOMEPAGE="http://zlab.bu.edu/clover/" -SRC_URI="http://zlab.bu.edu/~mfrith/downloads/${PN}-${MY_PV}.tar.gz http://zlab.bu.edu/clover/jaspar2005core" - -LICENSE="as-is" -SLOT="0" -IUSE="" -KEYWORDS="~x86" - -DEPEND="" -RDEPEND="" - -S="${WORKDIR}/${PN}-${MY_PV}" - -src_unpack() { - unpack ${PN}-${MY_PV}.tar.gz -} - -src_compile() { - sed -i "s:g++:$(tc-getCXX):; s:-Wall -O3:${CFLAGS}:" Makefile || die "sed failed" - emake || die "emake failed" -} - -src_install() { - dobin clover - dodir "/usr/share/${PN}" - insinto "/usr/share/${PN}" - doins ${DISTDIR}/jaspar2005core || die -} - -pkg_postinst() { - einfo "The motif library jaspar2005core has been installed in" - einfo " /usr/share/clover/jaspar2005core" - einfo "You can pass this library to clover for motif search, or use your own library." -} diff --git a/sci-biology/clover/files/digest-clover-2006.07.17 b/sci-biology/clover/files/digest-clover-2006.07.17 deleted file mode 100644 index c407197a6..000000000 --- a/sci-biology/clover/files/digest-clover-2006.07.17 +++ /dev/null @@ -1,6 +0,0 @@ -MD5 d0911be5da7d75164cb2d67f5d3f280d clover-2006-07-17.tar.gz 15610 -RMD160 e7f5c2b53afef2df292f9274b2a1ce2c1fbbc0c3 clover-2006-07-17.tar.gz 15610 -SHA256 e7b5b9fa8a341d49d9cf79a6d03ef0677a493f0c34a9a2f466a864575af91cb9 clover-2006-07-17.tar.gz 15610 -MD5 ab02ff3b3b4e79239d9176de9bda5e96 jaspar2005core 14913 -RMD160 6fe43472cc1a2e0389ad9290801db56488773d3e jaspar2005core 14913 -SHA256 498a560c67411789106b50ccdfd9bc41f571d77c2fe9bfba7e95128c0a122fe4 jaspar2005core 14913 diff --git a/sci-biology/clover/metadata.xml b/sci-biology/clover/metadata.xml deleted file mode 100644 index 7e3286984..000000000 --- a/sci-biology/clover/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>maintainer-wanted</herd> -</pkgmetadata> diff --git a/sci-biology/cluster/ChangeLog b/sci-biology/cluster/ChangeLog deleted file mode 100644 index acdb0cf3c..000000000 --- a/sci-biology/cluster/ChangeLog +++ /dev/null @@ -1,7 +0,0 @@ -# ChangeLog for sci-biology/cluster -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 09 Aug 2007; Jeff Gardner <je_fro@gentoo.org> ChangeLog: - Initial import of cluster-1.36 thanks to Favero Francesco - diff --git a/sci-biology/cluster/Manifest b/sci-biology/cluster/Manifest deleted file mode 100644 index 17e7ca9f3..000000000 --- a/sci-biology/cluster/Manifest +++ /dev/null @@ -1,20 +0,0 @@ -AUX cluster-1.36-helpmenu-fix.patch 1287 RMD160 825d60b78925cc1c1d914bb0cea1a9953080f0c5 SHA1 45c42fe412ad428359f773e99382546ab2cfc2f9 SHA256 a90c835dd2d4a8196bffa67737c5755a5c5bed1be62772a76fcf0229ffaf47d4 -MD5 65a6e7833e5a0a489c7b017464b7fedc files/cluster-1.36-helpmenu-fix.patch 1287 -RMD160 825d60b78925cc1c1d914bb0cea1a9953080f0c5 files/cluster-1.36-helpmenu-fix.patch 1287 -SHA256 a90c835dd2d4a8196bffa67737c5755a5c5bed1be62772a76fcf0229ffaf47d4 files/cluster-1.36-helpmenu-fix.patch 1287 -DIST cluster-1.36.tar.gz 971192 RMD160 72dea711c915074bca8d6186af285f8640bdfd43 SHA1 69bb0de8e5fb9d6bf5ab29b53d65b21ab97cc4ce SHA256 76f73740a2c8725e704780643cfac11875c957ba85254114946dccf3326caccf -EBUILD cluster-1.36.ebuild 1552 RMD160 9fb48feb8d7075ca4bf5a99e4ecf6e5c72b1a08c SHA1 7de36808ea8504f6ae63b0e7b863237d9527a898 SHA256 1dc66ec426ff85419e4577936de52b43ca006b1c58e274e3b661340d41344ff0 -MD5 aa681faa82772afcd8bbf73130fcae46 cluster-1.36.ebuild 1552 -RMD160 9fb48feb8d7075ca4bf5a99e4ecf6e5c72b1a08c cluster-1.36.ebuild 1552 -SHA256 1dc66ec426ff85419e4577936de52b43ca006b1c58e274e3b661340d41344ff0 cluster-1.36.ebuild 1552 -MISC ChangeLog 240 RMD160 c5b167761fa7fd0cb47ddbe0794f1851e367900f SHA1 6ea851b7d41fa95bb7dda862f416f9f9ed68acf8 SHA256 598dcd0f0044117a1049091c32988913dc7597b91cbc9b5ed715bb4d6d6d1c3e -MD5 e937b7d3a2c5647d0a573842b6c6d589 ChangeLog 240 -RMD160 c5b167761fa7fd0cb47ddbe0794f1851e367900f ChangeLog 240 -SHA256 598dcd0f0044117a1049091c32988913dc7597b91cbc9b5ed715bb4d6d6d1c3e ChangeLog 240 -MISC metadata.xml 380 RMD160 a1c3ba6e6674088b1f06f1d8554b0457d5a95154 SHA1 eaf44b343cd9b336365d6a5858e41cf62dadd39b SHA256 4893d94442ec3c749ddb0fef6e62257e98b435e1709d4e71fc0f6c4ceea52dc2 -MD5 95aa0e81b9a24708648671ec7f94d3a6 metadata.xml 380 -RMD160 a1c3ba6e6674088b1f06f1d8554b0457d5a95154 metadata.xml 380 -SHA256 4893d94442ec3c749ddb0fef6e62257e98b435e1709d4e71fc0f6c4ceea52dc2 metadata.xml 380 -MD5 16e58679fbea16fbaf0e00d97797b449 files/digest-cluster-1.36 238 -RMD160 2d7b7d05ffc8e775ce7ffc7ffd6dfcb8f824edc5 files/digest-cluster-1.36 238 -SHA256 d611e29bd0456213c139ed17e12d1faaf0912da5140f82b2daa0903eee4c241f files/digest-cluster-1.36 238 diff --git a/sci-biology/cluster/cluster-1.36.ebuild b/sci-biology/cluster/cluster-1.36.ebuild deleted file mode 100644 index 5af64c16b..000000000 --- a/sci-biology/cluster/cluster-1.36.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ -inherit autotools -SRC_URI="${P}.tar.gz" - -DESCRIPTION="Clustering software for microarray analysis" -HOMEPAGE="http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm#ctv" -LICENSE="" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="X" - -DEPEND="X? ( virtual/motif )" -RDEPEND="X? ( x11-misc/xdg-utils app-text/xpdf )" - -RESTRICT="fetch" - -pkg_nofetch() { - einfo "Please obtain ${P}.tar.gz from ${HOMEPAGE} and place it in ${DISTDIR}" -} - -src_unpack() { - unpack "${A}" - cd "${S}" - sed -i \ - -e 's:^docdir = $(prefix)/cluster/doc:docdir = @docdir@:' \ - -e 's:^htmldir = $(prefix)/cluster/html:htmldir = @htmldir@:' \ - -e 's:^imagedir = $(prefix)/cluster/html/images:imagedir = @htmldir@/images:' \ - -e 's:^fileformatdir = $(prefix)/cluster:fileformatdir = @docdir@:' \ - X11/Makefile.in || die "sed failed" - - epatch "${FILESDIR}/${P}-helpmenu-fix.patch" || die "failed to patch helpmenu" - -} - -src_compile() { - - econf $(use_with X x) \ - --docdir="/usr/share/doc/${P}" \ - --htmldir="/usr/share/doc/${P}/html" \ - || die "econf failed" - - emake || die "emake failed" -} - -src_install() { - cd ${S} - emake DESTDIR="${D}" install || die "Install failed" - - dodoc README COPYING AUTHORS ChangeLog NEWS TODO || die "failed to install docs" - insinto /usr/share/doc/${P}/examples - doins example/example.c example/README || die "failed to install docs" - insinto /usr/share/doc/${P} - doins doc/cluster.pdf || die "failed to install docs" - -} diff --git a/sci-biology/cluster/files/cluster-1.36-helpmenu-fix.patch b/sci-biology/cluster/files/cluster-1.36-helpmenu-fix.patch deleted file mode 100644 index 69f3a963e..000000000 --- a/sci-biology/cluster/files/cluster-1.36-helpmenu-fix.patch +++ /dev/null @@ -1,30 +0,0 @@ ---- X11/gui.c 2007-05-05 00:21:30.000000000 -0500 -+++ X11/gui.c-new 2007-08-09 04:25:53.000000000 -0500 -@@ -1786,15 +1786,15 @@ - { int item_no = (int) client_data; - switch (item_no) - { case CMD_HELP_HTMLHELP: -- { system("netscape "PREFIX"/cluster/html/index.html &"); -+ { system("xdg-open "PREFIX"/share/doc/cluster-1.36/html/index.html &"); - break; - } - case CMD_HELP_MANUAL: -- { system("acroread "PREFIX"/cluster/doc/cluster3.pdf &"); -+ { system("xpdf "PREFIX"/share/doc/cluster-1.36/cluster3.pdf &"); - break; - } - case CMD_HELP_DOWNLOAD: -- { system("netscape http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/manual/index.html &"); -+ { system("xdg-open http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/manual/index.html &"); - break; - } - case CMD_HELP_FILEFORMAT: -@@ -1852,7 +1852,7 @@ - XtManageChild(widget); - free(helptext); - n = 0; -- pixmap = XmGetPixmap(XtScreen(dialog),PREFIX"/cluster/format.xpm",0,0); -+ pixmap = XmGetPixmap(XtScreen(dialog),PREFIX"/share/doc/cluster-1.36/format.xpm",0,0); - XtSetArg(args[n], XmNx, 10); n++; - XtSetArg(args[n], XmNy, 410); n++; - XtSetArg(args[n],XmNlabelType, XmPIXMAP); n++; diff --git a/sci-biology/cluster/files/digest-cluster-1.36 b/sci-biology/cluster/files/digest-cluster-1.36 deleted file mode 100644 index 4611127da..000000000 --- a/sci-biology/cluster/files/digest-cluster-1.36 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 9333963ab3217bb3b51de5c491078563 cluster-1.36.tar.gz 971192 -RMD160 72dea711c915074bca8d6186af285f8640bdfd43 cluster-1.36.tar.gz 971192 -SHA256 76f73740a2c8725e704780643cfac11875c957ba85254114946dccf3326caccf cluster-1.36.tar.gz 971192 diff --git a/sci-biology/cluster/metadata.xml b/sci-biology/cluster/metadata.xml deleted file mode 100644 index 2971c5ba0..000000000 --- a/sci-biology/cluster/metadata.xml +++ /dev/null @@ -1,14 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>sci-biology</herd> -<maintainer> -<email>je_fro@gentoo.org</email> -<name>Jeff Gardner</name> -</maintainer> -<longdescription lang="en"> -Cluster provides an interface to access methods of gene expression data -analysis. -</longdescription> -</pkgmetadata> - diff --git a/sci-biology/generecon/ChangeLog b/sci-biology/generecon/ChangeLog deleted file mode 100644 index ff5a98428..000000000 --- a/sci-biology/generecon/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/generecon -# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -*generecon-1.2.1 (19 Apr 2006) - - 19 Apr 2006; Lucas Chiesa <lucas.chiesa@gmail.com>: - +generecon-1.2.1.ebuild, +metadata.xml, +ChangeLog, - Initial import. Thanks to Neil <nshephard@gmail.com> - for the initial ebuild. Closes bug #128514. diff --git a/sci-biology/generecon/Manifest b/sci-biology/generecon/Manifest deleted file mode 100644 index 83fec8d58..000000000 --- a/sci-biology/generecon/Manifest +++ /dev/null @@ -1,20 +0,0 @@ -AUX generecon-docfiles.patch 435 RMD160 ce732399b02f42a0089ea82ea240098dfb8207c5 SHA1 4f6ed16b9ce8f118b99a47d9e36ffa304e42e8bb SHA256 37fbf94d6716a489e6a59f119cf617b9ff024e612dc96323d2297f9c09360175 -MD5 537dc4e80ebe82b913290cfc7a0f6144 files/generecon-docfiles.patch 435 -RMD160 ce732399b02f42a0089ea82ea240098dfb8207c5 files/generecon-docfiles.patch 435 -SHA256 37fbf94d6716a489e6a59f119cf617b9ff024e612dc96323d2297f9c09360175 files/generecon-docfiles.patch 435 -DIST generecon-1.2.1.tar.gz 238270 RMD160 f625ec81db88556a33e76f63c5c242b70e951f0f SHA1 a1562a21eab88d6ac1b2d2c046b87414ff703d4b SHA256 b35496ab6baf0bda45dc7a934385441cc92bfac39cb0a261a541ad8b258ba446 -EBUILD generecon-1.2.1-r1.ebuild 1015 RMD160 0108cae8648d7e7831f18194e07f6796ac018fbc SHA1 7a77fcab817a6a70f4f7ae08ce71e9224d48ffa4 SHA256 b4b07aaab53f7a16cb2a1cc1b5c5d76df7198c2d012a25fe35a62de17b5cfb5f -MD5 c793459ba1d3a6a3ffc81dd783c9edb1 generecon-1.2.1-r1.ebuild 1015 -RMD160 0108cae8648d7e7831f18194e07f6796ac018fbc generecon-1.2.1-r1.ebuild 1015 -SHA256 b4b07aaab53f7a16cb2a1cc1b5c5d76df7198c2d012a25fe35a62de17b5cfb5f generecon-1.2.1-r1.ebuild 1015 -MISC ChangeLog 363 RMD160 19d0d4926d34d52c906e11fef60b3d7d713c0b4f SHA1 d3248b7ba9d5b2aa8af1c6c77802199041720c0e SHA256 9a3bb08c6357408656ecf892cbe5e25eb62f53211e8276237b383d7548755242 -MD5 29a1e620d057818eb5edbc12f4c1f9ac ChangeLog 363 -RMD160 19d0d4926d34d52c906e11fef60b3d7d713c0b4f ChangeLog 363 -SHA256 9a3bb08c6357408656ecf892cbe5e25eb62f53211e8276237b383d7548755242 ChangeLog 363 -MISC metadata.xml 261 RMD160 d7630eceb5ae049fa36c58ed3c9f6fe7780c15bf SHA1 6ded05d9eaded2a6b810b7f80dd2dc3270bbff8e SHA256 8bbae243cac9cf6fc1d24a0582390bd1184df161f4d7f87300874e6a7860b15c -MD5 5cfd1e62f34b60928bc68a829d31d4eb metadata.xml 261 -RMD160 d7630eceb5ae049fa36c58ed3c9f6fe7780c15bf metadata.xml 261 -SHA256 8bbae243cac9cf6fc1d24a0582390bd1184df161f4d7f87300874e6a7860b15c metadata.xml 261 -MD5 290f19d04f4c5d01712c2acb82451690 files/digest-generecon-1.2.1-r1 247 -RMD160 b8e2df20a2475c5a5d2866b0f7dff927a1021b5c files/digest-generecon-1.2.1-r1 247 -SHA256 e444905c55f0025a00372c2456d27b2b7cedfe82e03b7fd54807f26646903eed files/digest-generecon-1.2.1-r1 247 diff --git a/sci-biology/generecon/files/digest-generecon-1.2.1-r1 b/sci-biology/generecon/files/digest-generecon-1.2.1-r1 deleted file mode 100644 index 03adaf567..000000000 --- a/sci-biology/generecon/files/digest-generecon-1.2.1-r1 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 bda6f2a7c40ddbe5f694050a299ef6a4 generecon-1.2.1.tar.gz 238270 -RMD160 f625ec81db88556a33e76f63c5c242b70e951f0f generecon-1.2.1.tar.gz 238270 -SHA256 b35496ab6baf0bda45dc7a934385441cc92bfac39cb0a261a541ad8b258ba446 generecon-1.2.1.tar.gz 238270 diff --git a/sci-biology/generecon/files/generecon-docfiles.patch b/sci-biology/generecon/files/generecon-docfiles.patch deleted file mode 100644 index 79d63e73f..000000000 --- a/sci-biology/generecon/files/generecon-docfiles.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -Nuar generecon-1.2.1.orig/Makefile.am generecon-1.2.1/Makefile.am ---- generecon-1.2.1.orig/Makefile.am 2006-04-19 12:52:18.000000000 -0300 -+++ generecon-1.2.1/Makefile.am 2006-04-19 12:55:53.000000000 -0300 -@@ -31,7 +31,7 @@ - bin_PROGRAMS = generecon - - --docdir = ${prefix}/share/generecon/doc -+docdir = ${prefix}/share/doc/#PF# - dist_doc_DATA = - test_inputdir = ${prefix}/share/generecon/test-input - dist_test_input_DATA = diff --git a/sci-biology/generecon/generecon-1.2.1-r1.ebuild b/sci-biology/generecon/generecon-1.2.1-r1.ebuild deleted file mode 100644 index 7adfb5cf5..000000000 --- a/sci-biology/generecon/generecon-1.2.1-r1.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit eutils - -DESCRIPTION="Generecon performs linkage disequilibrium gene mapping based on coalescent theory using Bayesian Markov Chain Monte Carlo methods." -HOMEPAGE="http://www.daimi.au.dk/~mailund/GeneRecon/" -SRC_URI="http://www.daimi.au.dk/~mailund/GeneRecon/download/${P}.tar.gz" -SLOT="0" - -# License of the package. This must match the name of file(s) in -# /usr/portage/licenses/. For complex license combination see the developer -# docs on gentoo.org for details. -LICENSE="GPL-2" - -KEYWORDS="x86" - -DEPEND="dev-scheme/guile - sci-libs/gsl" - -src_unpack() { - unpack ${A} - sed 's|#PF#|'${PF}'|g' ${FILESDIR}/${PN}-docfiles.patch > ${PN}-docfiles.patch - - epatch ${PN}-docfiles.patch - - cd ${S} - pwd - einfo "Regenerating autotools files..." - aclocal || die "aclocal failed" - automake || die "automake failed" -} - -src_install() { - make DESTDIR=${D} install || die "make install failed" -} diff --git a/sci-biology/generecon/metadata.xml b/sci-biology/generecon/metadata.xml deleted file mode 100644 index 963198591..000000000 --- a/sci-biology/generecon/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> - <herd>sci</herd> - <maintainer> - <email>lucas.chiesa@gmail.com</email> - <name>Lucas Chiesa</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/glimmer/ChangeLog b/sci-biology/glimmer/ChangeLog deleted file mode 100644 index 2fc95e1e1..000000000 --- a/sci-biology/glimmer/ChangeLog +++ /dev/null @@ -1,11 +0,0 @@ -# ChangeLog for sci-biology/glimmer -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +glimmer-3.02.ebuild: - Mass import from sunrise - - 14 Mar 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +glimmer-3.02.ebuild, - +metadata.xml: - new package sci-biology/glimmer (bug 170895) - diff --git a/sci-biology/glimmer/Manifest b/sci-biology/glimmer/Manifest deleted file mode 100644 index 1b08c4db9..000000000 --- a/sci-biology/glimmer/Manifest +++ /dev/null @@ -1,16 +0,0 @@ -DIST glimmer302.tar.gz 5637075 RMD160 bc29bb045f7a4179504cb3843741393f42e11ab8 SHA1 e2f27fdab82cd8978f1452bfcd4c0287c52b77b7 SHA256 a1e422ee56f495f9f99e1741ba2043f026fc8182afcc47cb20cfd2d989537221 -EBUILD glimmer-3.02.ebuild 839 RMD160 5f3881415516349d932ea51632b8ae19f5e3c0af SHA1 979d34e653b1139a6400f694161133634d40ec69 SHA256 00f660e15cfe8084b3b65e488e5041743194722b7786ca114f22ec368b6e11e5 -MD5 2431066d7e43a58b06fdaff0e2f9bd85 glimmer-3.02.ebuild 839 -RMD160 5f3881415516349d932ea51632b8ae19f5e3c0af glimmer-3.02.ebuild 839 -SHA256 00f660e15cfe8084b3b65e488e5041743194722b7786ca114f22ec368b6e11e5 glimmer-3.02.ebuild 839 -MISC ChangeLog 365 RMD160 07fd0d884f3aebb2fc0c13de4d3f0df1d391ca85 SHA1 14ae9ea74f773515a0109a3c223a685e2c488cd3 SHA256 88f2c93b45b8e227684111cd0c2780229cc20937826784e70156b3146749a161 -MD5 ae0cdbff2c11ed541c08f17a9d9b3b2a ChangeLog 365 -RMD160 07fd0d884f3aebb2fc0c13de4d3f0df1d391ca85 ChangeLog 365 -SHA256 88f2c93b45b8e227684111cd0c2780229cc20937826784e70156b3146749a161 ChangeLog 365 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 -MD5 1e678929a9fec6632e227bdf2262e9a1 metadata.xml 170 -RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 metadata.xml 170 -SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 metadata.xml 170 -MD5 0598b7144226d863734ebb1b24afbf42 files/digest-glimmer-3.02 235 -RMD160 9847204829229587d689348ec41f339162f447c6 files/digest-glimmer-3.02 235 -SHA256 8f9193b635bdf44fde42e859c109f9b3d0edf3b5e1eba9ddea979671561ffedd files/digest-glimmer-3.02 235 diff --git a/sci-biology/glimmer/files/digest-glimmer-3.02 b/sci-biology/glimmer/files/digest-glimmer-3.02 deleted file mode 100644 index b724ad949..000000000 --- a/sci-biology/glimmer/files/digest-glimmer-3.02 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 3e933b79c7d019eb48fa87b9fda1e1ee glimmer302.tar.gz 5637075 -RMD160 bc29bb045f7a4179504cb3843741393f42e11ab8 glimmer302.tar.gz 5637075 -SHA256 a1e422ee56f495f9f99e1741ba2043f026fc8182afcc47cb20cfd2d989537221 glimmer302.tar.gz 5637075 diff --git a/sci-biology/glimmer/glimmer-3.02.ebuild b/sci-biology/glimmer/glimmer-3.02.ebuild deleted file mode 100644 index 2814ad994..000000000 --- a/sci-biology/glimmer/glimmer-3.02.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit versionator - -MY_PV=$(delete_all_version_separators) - -DESCRIPTION="An HMM-based microbial gene finding system from TIGR" -HOMEPAGE="http://www.cbcb.umd.edu/software/glimmer/" -SRC_URI="http://www.cbcb.umd.edu/software/${PN}/${PN}${MY_PV}.tar.gz" - -LICENSE="Artistic" -SLOT="0" -IUSE="" -KEYWORDS="~x86" - -DEPEND="" -RDEPEND="" - -S=${WORKDIR}/${PN}${PV} - -src_compile() { - sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \ - -e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths" - cd src - emake || die "emake failed" -} - -src_install() { - rm bin/test - dobin bin/* - - dodir /usr/share/${PN}/scripts - insinto /usr/share/${PN}/scripts - doins scripts/* - - dodoc glim302notes.pdf -} diff --git a/sci-biology/glimmer/metadata.xml b/sci-biology/glimmer/metadata.xml deleted file mode 100644 index 7e3286984..000000000 --- a/sci-biology/glimmer/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>maintainer-wanted</herd> -</pkgmetadata> diff --git a/sci-biology/glimmerhmm/ChangeLog b/sci-biology/glimmerhmm/ChangeLog deleted file mode 100644 index 918e4112f..000000000 --- a/sci-biology/glimmerhmm/ChangeLog +++ /dev/null @@ -1,16 +0,0 @@ -# ChangeLog for sci-biology/glimmerhmm -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> - +glimmerhmm-3.0.1.ebuild: - Mass import from sunrise - - 15 Mar 2007; Christian Faulhammer <opfer@gentoo.org> - glimmerhmm-3.0.1.ebuild: - Orthographic sex-up - - 14 Mar 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +glimmerhmm-3.0.1.ebuild, - +metadata.xml: - new package sci-biology/glimmerhmm (bug 170964) - diff --git a/sci-biology/glimmerhmm/Manifest b/sci-biology/glimmerhmm/Manifest deleted file mode 100644 index e07e63b79..000000000 --- a/sci-biology/glimmerhmm/Manifest +++ /dev/null @@ -1,16 +0,0 @@ -DIST GlimmerHMM-3.0.1.tar.gz 45475952 RMD160 273cb74458e3f444cd9f8ca9f6618335aea5465f SHA1 6caf10a3fb79660e48d88560869dee0394961f1a SHA256 c956838a398483003ff1af867c65aca082b82340d8b302b9ada77d1b246954e4 -EBUILD glimmerhmm-3.0.1.ebuild 1256 RMD160 63bbac5df129a0867aa0ab6e025710c8683cdcf6 SHA1 c517e20085e5e716435c0d29bd1a3bae9228e2d1 SHA256 0a9df33ae04c5b275999041573f0935b32be4797da0b48211e88dbe277d7dfe5 -MD5 660bd1edbd45fe60d64f23417d319a80 glimmerhmm-3.0.1.ebuild 1256 -RMD160 63bbac5df129a0867aa0ab6e025710c8683cdcf6 glimmerhmm-3.0.1.ebuild 1256 -SHA256 0a9df33ae04c5b275999041573f0935b32be4797da0b48211e88dbe277d7dfe5 glimmerhmm-3.0.1.ebuild 1256 -MISC ChangeLog 486 RMD160 7d213d91b90390472c3afbf1a921ccbbfc6111c3 SHA1 7c1d8b78c09b3c2344874ca9923aab99cf0656d8 SHA256 87dcfa56bc3f3a8f104c7fcf893596d6ab677a982af26651336a7b8854fd31f1 -MD5 6f733ec00f6a44d4d0e8c47297f1b91a ChangeLog 486 -RMD160 7d213d91b90390472c3afbf1a921ccbbfc6111c3 ChangeLog 486 -SHA256 87dcfa56bc3f3a8f104c7fcf893596d6ab677a982af26651336a7b8854fd31f1 ChangeLog 486 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 -MD5 1e678929a9fec6632e227bdf2262e9a1 metadata.xml 170 -RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 metadata.xml 170 -SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 metadata.xml 170 -MD5 6031057f170ba3e39d873476919294cf files/digest-glimmerhmm-3.0.1 256 -RMD160 30de1bc3c8be7819528bdbaea8be47a38d92b3a5 files/digest-glimmerhmm-3.0.1 256 -SHA256 a5ceb414b56313f97ef383cc3debda25408bcf877376fc456319a55e6f4f769e files/digest-glimmerhmm-3.0.1 256 diff --git a/sci-biology/glimmerhmm/files/digest-glimmerhmm-3.0.1 b/sci-biology/glimmerhmm/files/digest-glimmerhmm-3.0.1 deleted file mode 100644 index 9ab418485..000000000 --- a/sci-biology/glimmerhmm/files/digest-glimmerhmm-3.0.1 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 e98e0bad04507b7f661e6b9876c3d1f6 GlimmerHMM-3.0.1.tar.gz 45475952 -RMD160 273cb74458e3f444cd9f8ca9f6618335aea5465f GlimmerHMM-3.0.1.tar.gz 45475952 -SHA256 c956838a398483003ff1af867c65aca082b82340d8b302b9ada77d1b246954e4 GlimmerHMM-3.0.1.tar.gz 45475952 diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild deleted file mode 100644 index 61f3a2740..000000000 --- a/sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -MY_P=GlimmerHMM - -DESCRIPTION="An eukaryotic gene finding system from TIGR" -HOMEPAGE="http://www.cbcb.umd.edu/software/GlimmerHMM/" -SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/${MY_P}-${PV}.tar.gz" - -LICENSE="Artistic" -SLOT="0" -IUSE="" -KEYWORDS="~x86" - -DEPEND="" -RDEPEND="" - -S=${WORKDIR}/${MY_P} - -src_compile() { - sed -i -e 's|\(my $scriptdir=\)$FindBin::Bin|\1"/usr/share/'${PN}'/training_utils"|' \ - -e 's|\(use lib\) $FindBin::Bin|\1 "/usr/share/'${PN}'/lib"|' train/trainGlimmerHMM || die "sed failed" - sed -i 's/^CFLAGS[ ]*=.*//' */makefile - - cd sources - emake || die "emake failed in sources" - cd "${S}/train" || die "failed to cd" - emake || die "emake failed in train" -} - -src_install() { - dobin sources/glimmerhmm train/trainGlimmerHMM - - dodir /usr/share/${PN}/{lib,models,training_utils} - insinto /usr/share/${PN}/lib - doins train/*.pm - insinto /usr/share/${PN}/models - doins -r trained_dir/* - insinto /usr/share/${PN}/training_utils - insopts -m755 - doins train/{build{1,2,-icm,-icm-noframe},erfapp,falsecomp,findsites,karlin,score,score{2,ATG,ATG2,STOP,STOP2},splicescore} - - dodoc README.first train/readme.train -} diff --git a/sci-biology/glimmerhmm/metadata.xml b/sci-biology/glimmerhmm/metadata.xml deleted file mode 100644 index 7e3286984..000000000 --- a/sci-biology/glimmerhmm/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>maintainer-wanted</herd> -</pkgmetadata> diff --git a/sci-biology/gmap/ChangeLog b/sci-biology/gmap/ChangeLog deleted file mode 100644 index 6e87b45e7..000000000 --- a/sci-biology/gmap/ChangeLog +++ /dev/null @@ -1,31 +0,0 @@ -# ChangeLog for sci-biology/gmap -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 11 Sep 2007; weaver <weaver@horizon.ath.cx> +gmap-2007.07.16.ebuild: - version bump - - 30 May 2007; weaver <weaver@horizon.ath.cx> files/digest-gmap-2007.05.25, - Manifest: - upstream re-rolled tarball due to single bug, updating digests - - 29 May 2007; weaver <weaver@horizon.ath.cx> +gmap-2007.05.25.ebuild: - version bump - - 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> ChangeLog: - Mass import from sunrise - - 15 Apr 2007; Stefan Schweizer <genstef@gentoo.org> gmap-2006.12.18.ebuild: - Remove RESTRICT=mirror, gmap license allows redistribution - - 09 Jan 2007; Markus Ullmann <jokey@gentoo.org> -gmap-2006.12.12.ebuild: - Drop old - - 03 Jan 2007; Andrey Kislyuk (weaver) <weaver@horizon.ath.cx> - +gmap-2006.12.18.ebuild: - new version - - 12 Dec 2006; Andrey Kislyuk (weaver) <weaver@horizon.ath.cx> - +gmap-20060421.ebuild, +metadata.xml: - New ebuild, see Bug 135103 - diff --git a/sci-biology/gmap/Manifest b/sci-biology/gmap/Manifest deleted file mode 100644 index bddd171b4..000000000 --- a/sci-biology/gmap/Manifest +++ /dev/null @@ -1,32 +0,0 @@ -DIST gmap-2006-12-18.tar.gz 829170 RMD160 fb247cc2c792ebb49742b33eecec2352b75c5123 SHA1 d9f2f7248176897c153f15bc00029a703fed6c5a SHA256 992f9f2058f83b4a84ffb84c9aaba75fc18d8ccdb0a0be66086f7f94f3ba5675 -DIST gmap-2007-05-25.tar.gz 953535 RMD160 203ae638492522e9acea435b1128386b19185ec1 SHA1 c167fc0d50816caae5e964464bcb60abd6087e8d SHA256 f1488314856819940ca39f4f7f106e2099e43d29d7e95e047cee7771357ce506 -DIST gmap-2007-07-16.tar.gz 964986 RMD160 ea375b06eb6d14c0c4d2b2d07374f81792b81ccd SHA1 6862cd16b156720f374a967be6b9dc9f71878bc5 SHA256 9634bde9f2a59630561eee957bd2fc90a96e20d1859ca00180a16279ad8e40f1 -EBUILD gmap-2006.12.18.ebuild 589 RMD160 fb37510fd9269a5ae82e8e58c167cda5477bb94b SHA1 bda2d2d3b5d20803a141e8c0ab7da52f0a395839 SHA256 ca6bb5ca0e0443c308fb7b54313856c94f835dd4c9d5a3f5a6b6d60e658add54 -MD5 73bb62eca876fea0a2aa915e40999062 gmap-2006.12.18.ebuild 589 -RMD160 fb37510fd9269a5ae82e8e58c167cda5477bb94b gmap-2006.12.18.ebuild 589 -SHA256 ca6bb5ca0e0443c308fb7b54313856c94f835dd4c9d5a3f5a6b6d60e658add54 gmap-2006.12.18.ebuild 589 -EBUILD gmap-2007.05.25.ebuild 589 RMD160 fb37510fd9269a5ae82e8e58c167cda5477bb94b SHA1 bda2d2d3b5d20803a141e8c0ab7da52f0a395839 SHA256 ca6bb5ca0e0443c308fb7b54313856c94f835dd4c9d5a3f5a6b6d60e658add54 -MD5 73bb62eca876fea0a2aa915e40999062 gmap-2007.05.25.ebuild 589 -RMD160 fb37510fd9269a5ae82e8e58c167cda5477bb94b gmap-2007.05.25.ebuild 589 -SHA256 ca6bb5ca0e0443c308fb7b54313856c94f835dd4c9d5a3f5a6b6d60e658add54 gmap-2007.05.25.ebuild 589 -EBUILD gmap-2007.07.16.ebuild 589 RMD160 fb37510fd9269a5ae82e8e58c167cda5477bb94b SHA1 bda2d2d3b5d20803a141e8c0ab7da52f0a395839 SHA256 ca6bb5ca0e0443c308fb7b54313856c94f835dd4c9d5a3f5a6b6d60e658add54 -MD5 73bb62eca876fea0a2aa915e40999062 gmap-2007.07.16.ebuild 589 -RMD160 fb37510fd9269a5ae82e8e58c167cda5477bb94b gmap-2007.07.16.ebuild 589 -SHA256 ca6bb5ca0e0443c308fb7b54313856c94f835dd4c9d5a3f5a6b6d60e658add54 gmap-2007.07.16.ebuild 589 -MISC ChangeLog 1001 RMD160 5d1a59e49fe0f3048cdb9813d69678d81865c9cd SHA1 e9db8a958d3b2cfcfcf052884f14f6de154ad806 SHA256 922b20dc231bf2032749dd92237c7a0d644d5411d154770f89ff3e5271747b33 -MD5 de04957664b6882771a4a5a99a73f579 ChangeLog 1001 -RMD160 5d1a59e49fe0f3048cdb9813d69678d81865c9cd ChangeLog 1001 -SHA256 922b20dc231bf2032749dd92237c7a0d644d5411d154770f89ff3e5271747b33 ChangeLog 1001 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 -MD5 1e678929a9fec6632e227bdf2262e9a1 metadata.xml 170 -RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 metadata.xml 170 -SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 metadata.xml 170 -MD5 3105018bf8979d9f1b80cbc08d4a265d files/digest-gmap-2006.12.18 247 -RMD160 96744012a8023c6774884a9765561c933f8c971d files/digest-gmap-2006.12.18 247 -SHA256 f29e1072fadc0b29ff68666daed3acfa0db6654a5f53d3f262689a5380f9ee70 files/digest-gmap-2006.12.18 247 -MD5 9c6340106627755634ebc7ddb50549b2 files/digest-gmap-2007.05.25 247 -RMD160 0ac0751508d05b974e91b1fb2c70bbf636b3ba91 files/digest-gmap-2007.05.25 247 -SHA256 57c982b127d72c168d5257afa30b8c36317204bf33a231b8c8b9f90928158b2b files/digest-gmap-2007.05.25 247 -MD5 9c557610d38ea3647108bc87a13cdced files/digest-gmap-2007.07.16 247 -RMD160 d7fc8a2a0e92e803fbc9b2373bc041ae2f4f7bff files/digest-gmap-2007.07.16 247 -SHA256 666f055a6e1e199d4dc5ea3472299d445c894c6b004ba0d63dfc4710b1153a4c files/digest-gmap-2007.07.16 247 diff --git a/sci-biology/gmap/files/digest-gmap-2006.12.18 b/sci-biology/gmap/files/digest-gmap-2006.12.18 deleted file mode 100644 index 664f48e6c..000000000 --- a/sci-biology/gmap/files/digest-gmap-2006.12.18 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 05630cc5956d483da218c93b743e004a gmap-2006-12-18.tar.gz 829170 -RMD160 fb247cc2c792ebb49742b33eecec2352b75c5123 gmap-2006-12-18.tar.gz 829170 -SHA256 992f9f2058f83b4a84ffb84c9aaba75fc18d8ccdb0a0be66086f7f94f3ba5675 gmap-2006-12-18.tar.gz 829170 diff --git a/sci-biology/gmap/files/digest-gmap-2007.05.25 b/sci-biology/gmap/files/digest-gmap-2007.05.25 deleted file mode 100644 index c5a785ac4..000000000 --- a/sci-biology/gmap/files/digest-gmap-2007.05.25 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 8a5eff72f44a1ea9db1b30a611718449 gmap-2007-05-25.tar.gz 953535 -RMD160 203ae638492522e9acea435b1128386b19185ec1 gmap-2007-05-25.tar.gz 953535 -SHA256 f1488314856819940ca39f4f7f106e2099e43d29d7e95e047cee7771357ce506 gmap-2007-05-25.tar.gz 953535 diff --git a/sci-biology/gmap/files/digest-gmap-2007.07.16 b/sci-biology/gmap/files/digest-gmap-2007.07.16 deleted file mode 100644 index 64febb433..000000000 --- a/sci-biology/gmap/files/digest-gmap-2007.07.16 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 b8d8637323d0c1d22a1d7def4d5e0afa gmap-2007-07-16.tar.gz 964986 -RMD160 ea375b06eb6d14c0c4d2b2d07374f81792b81ccd gmap-2007-07-16.tar.gz 964986 -SHA256 9634bde9f2a59630561eee957bd2fc90a96e20d1859ca00180a16279ad8e40f1 gmap-2007-07-16.tar.gz 964986 diff --git a/sci-biology/gmap/gmap-2006.12.18.ebuild b/sci-biology/gmap/gmap-2006.12.18.ebuild deleted file mode 100644 index 2ee4ed983..000000000 --- a/sci-biology/gmap/gmap-2006.12.18.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit versionator - -MY_PV=$(replace_all_version_separators '-') - -DESCRIPTION="A Genomic Mapping and Alignment Program for mRNA and EST Sequences" -HOMEPAGE="http://www.gene.com/share/gmap/" -SRC_URI="http://www.gene.com/share/gmap/src/gmap-${MY_PV}.tar.gz" - -LICENSE="gmap" -SLOT="0" -IUSE="" -KEYWORDS="~x86" - -DEPEND="" -RDEPEND="" - -S="${WORKDIR}/gmap-${MY_PV}" - -src_install() { - emake install DESTDIR="${D}" || die "emake install failed" - dodoc AUTHORS ChangeLog README -} diff --git a/sci-biology/gmap/gmap-2007.05.25.ebuild b/sci-biology/gmap/gmap-2007.05.25.ebuild deleted file mode 100644 index 2ee4ed983..000000000 --- a/sci-biology/gmap/gmap-2007.05.25.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit versionator - -MY_PV=$(replace_all_version_separators '-') - -DESCRIPTION="A Genomic Mapping and Alignment Program for mRNA and EST Sequences" -HOMEPAGE="http://www.gene.com/share/gmap/" -SRC_URI="http://www.gene.com/share/gmap/src/gmap-${MY_PV}.tar.gz" - -LICENSE="gmap" -SLOT="0" -IUSE="" -KEYWORDS="~x86" - -DEPEND="" -RDEPEND="" - -S="${WORKDIR}/gmap-${MY_PV}" - -src_install() { - emake install DESTDIR="${D}" || die "emake install failed" - dodoc AUTHORS ChangeLog README -} diff --git a/sci-biology/gmap/gmap-2007.07.16.ebuild b/sci-biology/gmap/gmap-2007.07.16.ebuild deleted file mode 100644 index 2ee4ed983..000000000 --- a/sci-biology/gmap/gmap-2007.07.16.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit versionator - -MY_PV=$(replace_all_version_separators '-') - -DESCRIPTION="A Genomic Mapping and Alignment Program for mRNA and EST Sequences" -HOMEPAGE="http://www.gene.com/share/gmap/" -SRC_URI="http://www.gene.com/share/gmap/src/gmap-${MY_PV}.tar.gz" - -LICENSE="gmap" -SLOT="0" -IUSE="" -KEYWORDS="~x86" - -DEPEND="" -RDEPEND="" - -S="${WORKDIR}/gmap-${MY_PV}" - -src_install() { - emake install DESTDIR="${D}" || die "emake install failed" - dodoc AUTHORS ChangeLog README -} diff --git a/sci-biology/gmap/metadata.xml b/sci-biology/gmap/metadata.xml deleted file mode 100644 index 7e3286984..000000000 --- a/sci-biology/gmap/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>maintainer-wanted</herd> -</pkgmetadata> diff --git a/sci-biology/kalign/ChangeLog b/sci-biology/kalign/ChangeLog deleted file mode 100644 index 67a193de8..000000000 --- a/sci-biology/kalign/ChangeLog +++ /dev/null @@ -1,14 +0,0 @@ -# ChangeLog for sci-biology/kalign -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 29 Apr 2007; Jeff Gardner <je_fro@gentoo.org> ChangeLog: - Added ~amd64. - - 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +kalign-2.03.ebuild: - Mass import from sunrise - - 18 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +kalign-2.03.ebuild, - +metadata.xml: - New Ebuild for bug 175116 - diff --git a/sci-biology/kalign/Manifest b/sci-biology/kalign/Manifest deleted file mode 100644 index 61a877ea1..000000000 --- a/sci-biology/kalign/Manifest +++ /dev/null @@ -1,16 +0,0 @@ -DIST kalign_2.03.orig.tar.gz 114022 RMD160 e4677db9983b4bf567515c535dbd1f61cfdd70bd SHA1 c856d14b537a9139fc601e4de98870293a3aceb4 SHA256 710318fea8e3091da6fdedd16d6f94b9de069846afa502f4fe00d5d6b07511c0 -EBUILD kalign-2.03.ebuild 529 RMD160 02c6f1a4019b664be2263a9d03aec13c36c5e4aa SHA1 adfa98b67fe55fd56f3b767b39cb7c1d8e730355 SHA256 959b57056021948137f09c1404423e82e0e4ac30f274b942c2a110a20a22e6cf -MD5 8ac9cdf7c3106dedd256682e711cf51f kalign-2.03.ebuild 529 -RMD160 02c6f1a4019b664be2263a9d03aec13c36c5e4aa kalign-2.03.ebuild 529 -SHA256 959b57056021948137f09c1404423e82e0e4ac30f274b942c2a110a20a22e6cf kalign-2.03.ebuild 529 -MISC ChangeLog 343 RMD160 bcaff9788619b5f05e8fac144b7f233204414e09 SHA1 7de36f7cfc492dc5c995ad52116ffdec31e74bfe SHA256 4972a48319334ca6f4a9042b70d6dacaf88c729e5f9636c4b20f7c2fadef59df -MD5 4f0bdebfc8dc7dd844b3cd37146e5832 ChangeLog 343 -RMD160 bcaff9788619b5f05e8fac144b7f233204414e09 ChangeLog 343 -SHA256 4972a48319334ca6f4a9042b70d6dacaf88c729e5f9636c4b20f7c2fadef59df ChangeLog 343 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 -MD5 1e678929a9fec6632e227bdf2262e9a1 metadata.xml 170 -RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 metadata.xml 170 -SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 metadata.xml 170 -MD5 d84ac9676b1c40aa1a4a60dc45844ce3 files/digest-kalign-2.03 250 -RMD160 411b63d9fbd2948186ab62bb8e46ca8d1d3da690 files/digest-kalign-2.03 250 -SHA256 3956c75c0783a86fe6059bbc8c71ef2f98a9a1e61966eee3f142bc08f69cbcfe files/digest-kalign-2.03 250 diff --git a/sci-biology/kalign/files/digest-kalign-2.03 b/sci-biology/kalign/files/digest-kalign-2.03 deleted file mode 100644 index a292b31e0..000000000 --- a/sci-biology/kalign/files/digest-kalign-2.03 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 7ad1642cbb1853528c40d0fe6f235fce kalign_2.03.orig.tar.gz 114022 -RMD160 e4677db9983b4bf567515c535dbd1f61cfdd70bd kalign_2.03.orig.tar.gz 114022 -SHA256 710318fea8e3091da6fdedd16d6f94b9de069846afa502f4fe00d5d6b07511c0 kalign_2.03.orig.tar.gz 114022 diff --git a/sci-biology/kalign/kalign-2.03.ebuild b/sci-biology/kalign/kalign-2.03.ebuild deleted file mode 100644 index 79bea1903..000000000 --- a/sci-biology/kalign/kalign-2.03.ebuild +++ /dev/null @@ -1,27 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -DESCRIPTION="Global and progressive multiple sequence alignment" -HOMEPAGE="http://msa.cgb.ki.se/" -SRC_URI="mirror://debian/pool/main/k/kalign/${PN}_${PV}.orig.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -DEPEND="" -RDEPEND="" - -S="${WORKDIR}/${PN}" - -src_unpack() { - unpack ${A} - sed -i 's/^CFLAGS.*= -O9/CFLAGS := ${CFLAGS} -O3/' ${S}/Makefile.in -} - -src_install() { - dobin kalign - dodoc README -} diff --git a/sci-biology/kalign/metadata.xml b/sci-biology/kalign/metadata.xml deleted file mode 100644 index 7e3286984..000000000 --- a/sci-biology/kalign/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>maintainer-wanted</herd> -</pkgmetadata> diff --git a/sci-biology/mummer/ChangeLog b/sci-biology/mummer/ChangeLog deleted file mode 100644 index b0bc8509d..000000000 --- a/sci-biology/mummer/ChangeLog +++ /dev/null @@ -1,11 +0,0 @@ -# ChangeLog for sci-biology/mummer -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +mummer-3.19.ebuild: - Mass import from sunrise - - 07 Mar 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +mummer-3.19.ebuild, - +metadata.xml: - New package, Bug 169793 - diff --git a/sci-biology/mummer/Manifest b/sci-biology/mummer/Manifest deleted file mode 100644 index 094924a8a..000000000 --- a/sci-biology/mummer/Manifest +++ /dev/null @@ -1,16 +0,0 @@ -DIST MUMmer3.19.tar.gz 3141991 RMD160 54f3c692efb8bde7762c48186919754f2a8c178c SHA1 8906bab6bd43b307461de8b5f44122a115799533 SHA256 c590264e0def7de9259083de085f589ea39dc729d7f491790340b6b0abf3d6ab -EBUILD mummer-3.19.ebuild 1462 RMD160 5f8b0b879579bbb191e127ff8502cf85ad24a1d6 SHA1 4fe7b3203592abf4fef23576225389304983102a SHA256 a4b07705f9363862d0a22418b3afbf90a1170653b3417f6217d69febf0ea70a5 -MD5 6e44430e8985e9ae0c49344af52c4d8d mummer-3.19.ebuild 1462 -RMD160 5f8b0b879579bbb191e127ff8502cf85ad24a1d6 mummer-3.19.ebuild 1462 -SHA256 a4b07705f9363862d0a22418b3afbf90a1170653b3417f6217d69febf0ea70a5 mummer-3.19.ebuild 1462 -MISC ChangeLog 341 RMD160 3af940375849fd821b9a26f495ec4dfe0d0e43d2 SHA1 343e404673256e84eaa87aab34f23c2fd0e10677 SHA256 fba592d098848186f7e54967015b44ca01753a11251c505add0bd83d361364eb -MD5 583803d6dae0bbc9e2aa180ea0886f9a ChangeLog 341 -RMD160 3af940375849fd821b9a26f495ec4dfe0d0e43d2 ChangeLog 341 -SHA256 fba592d098848186f7e54967015b44ca01753a11251c505add0bd83d361364eb ChangeLog 341 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 -MD5 1e678929a9fec6632e227bdf2262e9a1 metadata.xml 170 -RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 metadata.xml 170 -SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 metadata.xml 170 -MD5 aecc1fc23d65ba16769fc4b9cd7661f1 files/digest-mummer-3.19 235 -RMD160 579c3b585978eb4b23bdb2029556279eb7b7f1a7 files/digest-mummer-3.19 235 -SHA256 03a7db30ce80070d11adee5be808e1752dccd73cbffc5b73c4b131430b63ecc3 files/digest-mummer-3.19 235 diff --git a/sci-biology/mummer/files/digest-mummer-3.19 b/sci-biology/mummer/files/digest-mummer-3.19 deleted file mode 100644 index 52ef1125f..000000000 --- a/sci-biology/mummer/files/digest-mummer-3.19 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 7e0aa1c7da68c31b66fda9687171d9ff MUMmer3.19.tar.gz 3141991 -RMD160 54f3c692efb8bde7762c48186919754f2a8c178c MUMmer3.19.tar.gz 3141991 -SHA256 c590264e0def7de9259083de085f589ea39dc729d7f491790340b6b0abf3d6ab MUMmer3.19.tar.gz 3141991 diff --git a/sci-biology/mummer/metadata.xml b/sci-biology/mummer/metadata.xml deleted file mode 100644 index 7e3286984..000000000 --- a/sci-biology/mummer/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>maintainer-wanted</herd> -</pkgmetadata> diff --git a/sci-biology/mummer/mummer-3.19.ebuild b/sci-biology/mummer/mummer-3.19.ebuild deleted file mode 100644 index a6b3e4c0c..000000000 --- a/sci-biology/mummer/mummer-3.19.ebuild +++ /dev/null @@ -1,48 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -MY_P=MUMmer${PV} -DESCRIPTION="A rapid whole genome aligner" -HOMEPAGE="http://mummer.sourceforge.net/" -SRC_URI="mirror://sourceforge/mummer/${MY_P}.tar.gz" - -LICENSE="Artistic" -SLOT="0" -IUSE="doc" -KEYWORDS="~x86" - -DEPEND="" -RDEPEND="" - -S=${WORKDIR}/${MY_P} - -src_compile() { - emake || die "emake failed" - - sed -i -e 's|\($AUX_BIN_DIR = "\).*"|\1/usr/bin"|' \ - -e 's|\($BIN_DIR = "\).*"|\1/usr/bin"|' \ - -e 's|\($SCRIPT_DIR = "\).*"|\1/usr/share/'${PN}'/lib"|' \ - -e 's|\(set bindir = \).*|\1/usr/bin|' \ - -e 's|\(set scriptdir = \).*|\1/usr/share/'${PN}'/scripts|' \ - -e 's|\(use lib "\).*"|\1/usr/share/'${PN}'/lib"|' \ - scripts/* exact-tandems mapview mummerplot nucmer promer run-mummer{1,3} || die "Failed to replace paths" - sed -i 's|$bindir/annotate|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh -} - -src_install() { - dobin nucmer2xfig show-coords mapview show-snps run-mummer{1,3} \ - exact-tandems promer repeat-match show-aligns gaps mummer \ - show-tiling mgaps nucmer mummerplot delta-filter combineMUMs aux_bin/* - newbin annotate mummer-annotate - - dodir /usr/share/${PN}/{lib,scripts} - insinto /usr/share/${PN}/scripts - doins scripts/{*.awk,*.csh,*.pl} - insinto /usr/share/${PN}/lib - doins scripts/Foundation.pm - - dodoc ACKNOWLEDGEMENTS ChangeLog README - insinto /usr/share/doc/${PF} - use doc && doins -r docs -} diff --git a/sci-biology/phrap/ChangeLog b/sci-biology/phrap/ChangeLog deleted file mode 100644 index ad24df867..000000000 --- a/sci-biology/phrap/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/phrap -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> - +phrap-0.990329.ebuild: - Mass import from sunrise - - 20 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +phrap-0.990329.ebuild, - +metadata.xml: - new package (bug 114094) - diff --git a/sci-biology/phrap/Manifest b/sci-biology/phrap/Manifest deleted file mode 100644 index b91e36473..000000000 --- a/sci-biology/phrap/Manifest +++ /dev/null @@ -1,16 +0,0 @@ -DIST phrap-distrib.tar.Z 366163 RMD160 f6d15059903868b907df225b9022b47957f4004a SHA1 69d9343d1d3bc7edcab2ebca222370fc9db7b9f7 SHA256 e0be79818e3a8ca17391f42cc0ffbaf1a63299c8845a0b9ac3aaeb3cac641fcc -EBUILD phrap-0.990329.ebuild 864 RMD160 8b68c2d90e42141a40be209940becdaa49905a86 SHA1 2d932bf847b0caf4b29bdd070a3b45bf6667b59d SHA256 4a45b1a66fee1b89b5ef05ab43e64302092c84fba3860459a4224fd7ed92c51b -MD5 4a1adcef5c69fe9cbf938427605a9a15 phrap-0.990329.ebuild 864 -RMD160 8b68c2d90e42141a40be209940becdaa49905a86 phrap-0.990329.ebuild 864 -SHA256 4a45b1a66fee1b89b5ef05ab43e64302092c84fba3860459a4224fd7ed92c51b phrap-0.990329.ebuild 864 -MISC ChangeLog 349 RMD160 df3f1863d3b262b9e132f56cca3ef29c32abec3a SHA1 fab185ba0db30f7e38348a51c320e18a07bfd3c5 SHA256 7f9bdafcf31c81b9645bbbe686713674401db183400afc50fe7645e362a0b0e6 -MD5 fe91acfe41cdb2b1bf6c9cda15f70023 ChangeLog 349 -RMD160 df3f1863d3b262b9e132f56cca3ef29c32abec3a ChangeLog 349 -SHA256 7f9bdafcf31c81b9645bbbe686713674401db183400afc50fe7645e362a0b0e6 ChangeLog 349 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 -MD5 1e678929a9fec6632e227bdf2262e9a1 metadata.xml 170 -RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 metadata.xml 170 -SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 metadata.xml 170 -MD5 ff974aab20ef25dcbd88133eb69a3050 files/digest-phrap-0.990329 238 -RMD160 0b184a131052786397b0ba8d5d426290710b4b6b files/digest-phrap-0.990329 238 -SHA256 f6fe89aa7f79d89a054545bbd328c858d58f0df88fae08af5873f6c58480b699 files/digest-phrap-0.990329 238 diff --git a/sci-biology/phrap/files/digest-phrap-0.990329 b/sci-biology/phrap/files/digest-phrap-0.990329 deleted file mode 100644 index 20d49a807..000000000 --- a/sci-biology/phrap/files/digest-phrap-0.990329 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 35175595801cafd22ec348fb9dba0ce4 phrap-distrib.tar.Z 366163 -RMD160 f6d15059903868b907df225b9022b47957f4004a phrap-distrib.tar.Z 366163 -SHA256 e0be79818e3a8ca17391f42cc0ffbaf1a63299c8845a0b9ac3aaeb3cac641fcc phrap-distrib.tar.Z 366163 diff --git a/sci-biology/phrap/metadata.xml b/sci-biology/phrap/metadata.xml deleted file mode 100644 index 7e3286984..000000000 --- a/sci-biology/phrap/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>maintainer-wanted</herd> -</pkgmetadata> diff --git a/sci-biology/phrap/phrap-0.990329.ebuild b/sci-biology/phrap/phrap-0.990329.ebuild deleted file mode 100644 index 06cffa641..000000000 --- a/sci-biology/phrap/phrap-0.990329.ebuild +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -DESCRIPTION="Phrap, swat, cross_match: Shotgun assembly and alignment utilities" -HOMEPAGE="http://www.phrap.org/" -SRC_URI="phrap-distrib.tar.Z" - -LICENSE="phrap" -SLOT="0" -KEYWORDS="~x86" -IUSE="" - -DEPEND="" -RDEPEND="" - -S="${WORKDIR}" - -RESTRICT="fetch" - -pkg_nofetch() { - einfo "Please visit http://www.phrap.org/phredphrapconsed.html and obtain the file" - einfo '"distrib.tar.Z", then rename it to "phrap-distrib.tar.Z" and put it in' - einfo "${DISTDIR}" -} - -src_compile() { - sed -i 's/CFLAGS=/#CFLAGS=/' makefile - sed -i 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' phrapview - emake || die "emake failed" -} - -src_install() { - dobin cluster cross_match loco phrap phrapview swat - for i in {general,phrap,swat}.doc ; do - newdoc ${i} ${i}.txt - done -} diff --git a/sci-biology/proda/ChangeLog b/sci-biology/proda/ChangeLog deleted file mode 100644 index 7ca249fa6..000000000 --- a/sci-biology/proda/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/proda -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +proda-1.0.ebuild: - Mass import from sunrise - - 22 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +proda-1.0.ebuild, +metadata.xml: - new package (bug 175524) - diff --git a/sci-biology/proda/Manifest b/sci-biology/proda/Manifest deleted file mode 100644 index 2b789efde..000000000 --- a/sci-biology/proda/Manifest +++ /dev/null @@ -1,16 +0,0 @@ -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 -MD5 22682139eeb32de1232bd4f3d7456da0 proda-1.0.ebuild 703 -RMD160 46c755309e2925f3ebcc6ede718cd7b3d38c8469 proda-1.0.ebuild 703 -SHA256 8c454b35cafb73ca9c77662f922cff590498d39dafca97bbf2a4803e8d8c6524 proda-1.0.ebuild 703 -MISC ChangeLog 335 RMD160 913d0c1816d44d2b575580909498c0ab71a2d16c SHA1 0d4cb7d8379e35695dc9f76df4d6120bd1d7cbbc SHA256 c9a0ed83283201f9dc4e644e83668eb162f6be98cf08e9b55c3df4748355c85d -MD5 5d191f83083ca000ac4f86904fa8cd4e ChangeLog 335 -RMD160 913d0c1816d44d2b575580909498c0ab71a2d16c ChangeLog 335 -SHA256 c9a0ed83283201f9dc4e644e83668eb162f6be98cf08e9b55c3df4748355c85d ChangeLog 335 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 -MD5 1e678929a9fec6632e227bdf2262e9a1 metadata.xml 170 -RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 metadata.xml 170 -SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 metadata.xml 170 -MD5 d66b9a5871deb48c5aebd2e205314e86 files/digest-proda-1.0 226 -RMD160 b047cfb9499fabf3e38310ecb357c0139bf23a7a files/digest-proda-1.0 226 -SHA256 cdfd52e024fa633e85826e1b4d6dac73adcbe64588f1868059bfd1e0231818c8 files/digest-proda-1.0 226 diff --git a/sci-biology/proda/files/digest-proda-1.0 b/sci-biology/proda/files/digest-proda-1.0 deleted file mode 100644 index 6d0162087..000000000 --- a/sci-biology/proda/files/digest-proda-1.0 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 99a0c04983d043f70e74b33ba6f38018 proda_1_0.tar.gz 38868 -RMD160 b024496c935cebb74d50479d8cdeacce820358b1 proda_1_0.tar.gz 38868 -SHA256 439a93bf35e1a29ac1d5dde51e61f2cb174618596afaaaaa27d33a8ea1868a08 proda_1_0.tar.gz 38868 diff --git a/sci-biology/proda/metadata.xml b/sci-biology/proda/metadata.xml deleted file mode 100644 index 7e3286984..000000000 --- a/sci-biology/proda/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>maintainer-wanted</herd> -</pkgmetadata> diff --git a/sci-biology/proda/proda-1.0.ebuild b/sci-biology/proda/proda-1.0.ebuild deleted file mode 100644 index f38a59413..000000000 --- a/sci-biology/proda/proda-1.0.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit versionator - -MY_PV=$(replace_all_version_separators '_') - -DESCRIPTION="Multiple alignment of protein sequences with repeated and shuffled elements" -HOMEPAGE="http://proda.stanford.edu/" -SRC_URI="http://proda.stanford.edu/proda_${MY_PV}.tar.gz" - -LICENSE="public-domain" -SLOT="0" -IUSE="" -KEYWORDS="~x86" - -DEPEND="" -RDEPEND="" - -S="${WORKDIR}/${PN}" - -src_unpack() { - unpack ${A} - sed -i -e 's/^\(CXXFLAGS =\)/#\1/' \ - -e 's/#CXXFLAGS = \(-O3.*$(OTHERFLAGS) -funroll-loops\)/CXXFLAGS := ${CXXFLAGS} \1/' \ - "${S}/Makefile" || die "sed failed" -} - -src_install() { - dobin proda -} diff --git a/sci-biology/repeatmasker-libraries/ChangeLog b/sci-biology/repeatmasker-libraries/ChangeLog deleted file mode 100644 index 6314ec8cb..000000000 --- a/sci-biology/repeatmasker-libraries/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/repeatmasker-libraries -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> - +repeatmasker-libraries-20061006.ebuild: - Mass import from sunrise - - 20 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> - +repeatmasker-libraries-20061006.ebuild, +metadata.xml: - new package (bug 114096) - diff --git a/sci-biology/repeatmasker-libraries/Manifest b/sci-biology/repeatmasker-libraries/Manifest deleted file mode 100644 index f8676f39e..000000000 --- a/sci-biology/repeatmasker-libraries/Manifest +++ /dev/null @@ -1,16 +0,0 @@ -DIST repeatmaskerlibraries-20061006.tar.gz 5673785 RMD160 ea08ba4dfd49462b92ea9c6ffe64777ec67144d0 SHA1 5cb34e5c9a968f7e6b4a38c642856827469b857c SHA256 a3813d6e1960954f739ec3bb97cf56e9de4e238e420c28caf13c62cbbe247c4b -EBUILD repeatmasker-libraries-20061006.ebuild 732 RMD160 dee404c6e4f28821b214c4d9900ff700681d9d02 SHA1 df3b98700d4a123cbdfdcdd458a7349ba2e33e26 SHA256 07726f54d11b2d51a951f4af72bce3cd0e9c4d2b64db1ad801640fa3772b4bee -MD5 64047993e47f8d8eb4ee89de9b997cd0 repeatmasker-libraries-20061006.ebuild 732 -RMD160 dee404c6e4f28821b214c4d9900ff700681d9d02 repeatmasker-libraries-20061006.ebuild 732 -SHA256 07726f54d11b2d51a951f4af72bce3cd0e9c4d2b64db1ad801640fa3772b4bee repeatmasker-libraries-20061006.ebuild 732 -MISC ChangeLog 400 RMD160 a7b967a97f44050f6aecf9b38cdb5b92153840a9 SHA1 d0acfd86dca1bd200621949093c8487155fb2f62 SHA256 65b876add1d030a87ba29b8aba86bf7ced4e3aa90b100a6b79bf9241e2b9cbcf -MD5 11aa8806469c87e2115220185dcba76b ChangeLog 400 -RMD160 a7b967a97f44050f6aecf9b38cdb5b92153840a9 ChangeLog 400 -SHA256 65b876add1d030a87ba29b8aba86bf7ced4e3aa90b100a6b79bf9241e2b9cbcf ChangeLog 400 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 -MD5 1e678929a9fec6632e227bdf2262e9a1 metadata.xml 170 -RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 metadata.xml 170 -SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 metadata.xml 170 -MD5 aabf0ed56a1c19284d0f8b5cadd67bfa files/digest-repeatmasker-libraries-20061006 295 -RMD160 0178405e653cd56670f004d34bf223a67d0eb084 files/digest-repeatmasker-libraries-20061006 295 -SHA256 8b025628149fa976ca845cb917f7d425652e91c5e28935a37e11a0a5902a459c files/digest-repeatmasker-libraries-20061006 295 diff --git a/sci-biology/repeatmasker-libraries/files/digest-repeatmasker-libraries-20061006 b/sci-biology/repeatmasker-libraries/files/digest-repeatmasker-libraries-20061006 deleted file mode 100644 index 002d19366..000000000 --- a/sci-biology/repeatmasker-libraries/files/digest-repeatmasker-libraries-20061006 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 65ca44b2b3e784ec764d6b67d0d9f8a3 repeatmaskerlibraries-20061006.tar.gz 5673785 -RMD160 ea08ba4dfd49462b92ea9c6ffe64777ec67144d0 repeatmaskerlibraries-20061006.tar.gz 5673785 -SHA256 a3813d6e1960954f739ec3bb97cf56e9de4e238e420c28caf13c62cbbe247c4b repeatmaskerlibraries-20061006.tar.gz 5673785 diff --git a/sci-biology/repeatmasker-libraries/metadata.xml b/sci-biology/repeatmasker-libraries/metadata.xml deleted file mode 100644 index 7e3286984..000000000 --- a/sci-biology/repeatmasker-libraries/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>maintainer-wanted</herd> -</pkgmetadata> diff --git a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20061006.ebuild b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20061006.ebuild deleted file mode 100644 index 6e1d528ce..000000000 --- a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20061006.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -DESCRIPTION="A special version of RepBase used by RepeatMasker" -HOMEPAGE="http://repeatmasker.org/" -SRC_URI="repeatmaskerlibraries-${PV}.tar.gz" - -LICENSE="as-is" -SLOT="0" -KEYWORDS="~x86" -IUSE="" - -DEPEND="" -RDEPEND="" - -S="${WORKDIR}/Libraries" - -RESTRICT="fetch" - -pkg_nofetch() { - einfo "Please register and download repeatmaskerlibraries-${PV}.tar.gz" - einfo 'at http://www.girinst.org/' - einfo '(select the "Repbase Update - RepeatMasker edition" link)' - einfo 'and place it in '${DISTDIR} -} - -src_install() { - dodir /usr/share/repeatmasker/Libraries - insinto /usr/share/repeatmasker/Libraries - doins "${S}/"* -} diff --git a/sci-biology/repeatmasker/ChangeLog b/sci-biology/repeatmasker/ChangeLog deleted file mode 100644 index 1c7082d50..000000000 --- a/sci-biology/repeatmasker/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/repeatmasker -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> - +repeatmasker-3.1.7.ebuild: - Mass import from sunrise - - 20 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +repeatmasker-3.1.7.ebuild, - +metadata.xml: - new package (bug 114096) - diff --git a/sci-biology/repeatmasker/Manifest b/sci-biology/repeatmasker/Manifest deleted file mode 100644 index 687ba7881..000000000 --- a/sci-biology/repeatmasker/Manifest +++ /dev/null @@ -1,16 +0,0 @@ -DIST RepeatMasker-open-3-1-7.tar.gz 8197799 RMD160 fda43f7e3ebe3dbf655b3071e93e6d47fdb8f1e3 SHA1 f36f09f2d4173437ac5eb090ea471b95fdfa832b SHA256 56c2866f7e489e5f606872ff97b509ae29e2b8816b8fd2ad0938edb7c6f788b8 -EBUILD repeatmasker-3.1.7.ebuild 1257 RMD160 dbc84c1ae3d41eaaf785199a665a12b0485053d4 SHA1 e3eb4f37c5683863702f11e18219e72fe3859bed SHA256 e8aca73edea668ad3a5f44ede1402fa65b6c1e5116572189c391a50850c6ae2c -MD5 956cae84557800d6c95e712926c9e389 repeatmasker-3.1.7.ebuild 1257 -RMD160 dbc84c1ae3d41eaaf785199a665a12b0485053d4 repeatmasker-3.1.7.ebuild 1257 -SHA256 e8aca73edea668ad3a5f44ede1402fa65b6c1e5116572189c391a50850c6ae2c repeatmasker-3.1.7.ebuild 1257 -MISC ChangeLog 364 RMD160 e1877e532b0e93379bc19763efdf5b7358257cc9 SHA1 28c87840dc383e8b463c91888b644b2084398ea3 SHA256 179cbb0e848c489075df2c00191e97c5b9bf1cb55b564548a958c2ab2c063584 -MD5 bd8e377c8f80129cdb99bf8c782acf47 ChangeLog 364 -RMD160 e1877e532b0e93379bc19763efdf5b7358257cc9 ChangeLog 364 -SHA256 179cbb0e848c489075df2c00191e97c5b9bf1cb55b564548a958c2ab2c063584 ChangeLog 364 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 -MD5 1e678929a9fec6632e227bdf2262e9a1 metadata.xml 170 -RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 metadata.xml 170 -SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 metadata.xml 170 -MD5 b9174bf38df7183f531cd70d0d632398 files/digest-repeatmasker-3.1.7 274 -RMD160 ec16d4108ead1718bd87b747216101b5f927cb17 files/digest-repeatmasker-3.1.7 274 -SHA256 fb42ae786b0974ae5f923335c6f985f9e766378d65ad42d76f50368a5c85c496 files/digest-repeatmasker-3.1.7 274 diff --git a/sci-biology/repeatmasker/files/digest-repeatmasker-3.1.7 b/sci-biology/repeatmasker/files/digest-repeatmasker-3.1.7 deleted file mode 100644 index cd87a7a2c..000000000 --- a/sci-biology/repeatmasker/files/digest-repeatmasker-3.1.7 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 2b3f5055eeae3cdf6c110d77ae10eafc RepeatMasker-open-3-1-7.tar.gz 8197799 -RMD160 fda43f7e3ebe3dbf655b3071e93e6d47fdb8f1e3 RepeatMasker-open-3-1-7.tar.gz 8197799 -SHA256 56c2866f7e489e5f606872ff97b509ae29e2b8816b8fd2ad0938edb7c6f788b8 RepeatMasker-open-3-1-7.tar.gz 8197799 diff --git a/sci-biology/repeatmasker/metadata.xml b/sci-biology/repeatmasker/metadata.xml deleted file mode 100644 index 7e3286984..000000000 --- a/sci-biology/repeatmasker/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>maintainer-wanted</herd> -</pkgmetadata> diff --git a/sci-biology/repeatmasker/repeatmasker-3.1.7.ebuild b/sci-biology/repeatmasker/repeatmasker-3.1.7.ebuild deleted file mode 100644 index d3ff1ce82..000000000 --- a/sci-biology/repeatmasker/repeatmasker-3.1.7.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit versionator - -MY_PV=$(replace_all_version_separators '-') - -DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA" -HOMEPAGE="http://repeatmasker.org/" -SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz" - -LICENSE="OSL-2.1" -SLOT="0" -KEYWORDS="~x86" -IUSE="" - -DEPEND="" -RDEPEND="sci-biology/phrap - sci-biology/repeatmasker-libraries" - -S="${WORKDIR}/RepeatMasker" - -src_compile() { - sed -i 's/system( "clear" );//' "${S}/configure" - cat << END | "${S}/configure" || die "configure failed" - -/usr/bin -/usr/share/${PN} -1 -/usr/bin -Y -4 -END - sed -i '/$REPEATMASKER_DIR/ s|$FindBin::RealBin|/usr/share/'${PN}'|' "${S}/RepeatMaskerConfig.pm" || die "sed failed" - sed -i 's|use lib $FindBin::RealBin;|use lib "/usr/share/'${PN}'/lib";|' "${S}"/{DateRepeats,ProcessRepeats,RepeatMasker} || die "sed failed" -} - -src_install() { - dobin DateRepeats ProcessRepeats RepeatMasker - - dodir /usr/share/${PN}/lib - insinto /usr/share/${PN}/lib - doins "${S}"/*.pm - - insinto /usr/share/${PN} - doins -r util Matrices - keepdir /usr/share/${PN}/Libraries - - dodoc README INSTALL repeatmasker.help daterepeats.help -} diff --git a/sci-biology/sibsim4/ChangeLog b/sci-biology/sibsim4/ChangeLog deleted file mode 100644 index 83fc95f4a..000000000 --- a/sci-biology/sibsim4/ChangeLog +++ /dev/null @@ -1,14 +0,0 @@ -# ChangeLog for sci-biology/sibsim4 -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 11 Sep 2007; weaver <weaver@horizon.ath.cx> +sibsim4-0.15.ebuild: - version bump - - 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +sibsim4-0.14.ebuild: - Mass import from sunrise - - 18 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +sibsim4-0.14.ebuild, - +metadata.xml: - new package (bug 175143) - diff --git a/sci-biology/sibsim4/Manifest b/sci-biology/sibsim4/Manifest deleted file mode 100644 index 40a2c2acb..000000000 --- a/sci-biology/sibsim4/Manifest +++ /dev/null @@ -1,24 +0,0 @@ -DIST SIBsim4-0.14.tar.gz 28956 RMD160 7e54d8973d750d80516c3cc2ce358230e3e8c4cf SHA1 ee4215b191b494074df4fe33088097e00e789393 SHA256 15c0493ddc21cb4086bcc2f72d6e7ac470256cd8d87605de359b59a853fb9596 -DIST SIBsim4-0.15.tar.gz 29090 RMD160 b9c56dd5bc2c69a2eefce7b15aa064d53c5ee8f0 SHA1 c0660daa7b95d986fc08dd6247014bbf3631cdd5 SHA256 d2b9c40d5935f1dc2bd66a65f80a907e0cfa7d317d304090ad32aa28b9f46a1b -EBUILD sibsim4-0.14.ebuild 542 RMD160 272b1b10dbd5346f28615b60b3293084da1c968e SHA1 3ec8dd7a03def6ffca466ab4cb1c104694708834 SHA256 b2ce925f5529d246dc4bcd9744889e0f3bcc9be7ff4041c8b119694bfea8a07b -MD5 05729babe5c14d6cb34049e7d9de7696 sibsim4-0.14.ebuild 542 -RMD160 272b1b10dbd5346f28615b60b3293084da1c968e sibsim4-0.14.ebuild 542 -SHA256 b2ce925f5529d246dc4bcd9744889e0f3bcc9be7ff4041c8b119694bfea8a07b sibsim4-0.14.ebuild 542 -EBUILD sibsim4-0.15.ebuild 542 RMD160 272b1b10dbd5346f28615b60b3293084da1c968e SHA1 3ec8dd7a03def6ffca466ab4cb1c104694708834 SHA256 b2ce925f5529d246dc4bcd9744889e0f3bcc9be7ff4041c8b119694bfea8a07b -MD5 05729babe5c14d6cb34049e7d9de7696 sibsim4-0.15.ebuild 542 -RMD160 272b1b10dbd5346f28615b60b3293084da1c968e sibsim4-0.15.ebuild 542 -SHA256 b2ce925f5529d246dc4bcd9744889e0f3bcc9be7ff4041c8b119694bfea8a07b sibsim4-0.15.ebuild 542 -MISC ChangeLog 429 RMD160 f0cac89ceeef990602eb76883532e934c0b19851 SHA1 a3a863686f2477f003b3a94aecc01b6b708750f1 SHA256 a99f78b1ab05bb2504312d4f3d0e90b1e64b5573768d8a7a65d2489aebca4ed6 -MD5 9b3d7b0ad4a40db64b76e95debe86ccd ChangeLog 429 -RMD160 f0cac89ceeef990602eb76883532e934c0b19851 ChangeLog 429 -SHA256 a99f78b1ab05bb2504312d4f3d0e90b1e64b5573768d8a7a65d2489aebca4ed6 ChangeLog 429 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 -MD5 1e678929a9fec6632e227bdf2262e9a1 metadata.xml 170 -RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 metadata.xml 170 -SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 metadata.xml 170 -MD5 800b79024b4b386017dac71d76999d9f files/digest-sibsim4-0.14 235 -RMD160 7744aa21f20c76c2038c18d72045cffdd8467b45 files/digest-sibsim4-0.14 235 -SHA256 93ae4b12c5399bb383e443a5a1ef2c44bdac1ffcc2b014d819fef71c077ead08 files/digest-sibsim4-0.14 235 -MD5 f1db1ddcb44150a0fb642bb36126d9e5 files/digest-sibsim4-0.15 235 -RMD160 4e7b441cbfad17958cc84e458a21db33c9d48a7b files/digest-sibsim4-0.15 235 -SHA256 9489f844fbc15a156541911e2fe5f8145b6cbd303b4a430d95eca0031bc01c69 files/digest-sibsim4-0.15 235 diff --git a/sci-biology/sibsim4/files/digest-sibsim4-0.14 b/sci-biology/sibsim4/files/digest-sibsim4-0.14 deleted file mode 100644 index a431daadd..000000000 --- a/sci-biology/sibsim4/files/digest-sibsim4-0.14 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 b63af91d9cacf7d4f557d72119f934e5 SIBsim4-0.14.tar.gz 28956 -RMD160 7e54d8973d750d80516c3cc2ce358230e3e8c4cf SIBsim4-0.14.tar.gz 28956 -SHA256 15c0493ddc21cb4086bcc2f72d6e7ac470256cd8d87605de359b59a853fb9596 SIBsim4-0.14.tar.gz 28956 diff --git a/sci-biology/sibsim4/files/digest-sibsim4-0.15 b/sci-biology/sibsim4/files/digest-sibsim4-0.15 deleted file mode 100644 index 02db39a0a..000000000 --- a/sci-biology/sibsim4/files/digest-sibsim4-0.15 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 4cef55d0a357c047989e003872d5e142 SIBsim4-0.15.tar.gz 29090 -RMD160 b9c56dd5bc2c69a2eefce7b15aa064d53c5ee8f0 SIBsim4-0.15.tar.gz 29090 -SHA256 d2b9c40d5935f1dc2bd66a65f80a907e0cfa7d317d304090ad32aa28b9f46a1b SIBsim4-0.15.tar.gz 29090 diff --git a/sci-biology/sibsim4/metadata.xml b/sci-biology/sibsim4/metadata.xml deleted file mode 100644 index 7e3286984..000000000 --- a/sci-biology/sibsim4/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>maintainer-wanted</herd> -</pkgmetadata> diff --git a/sci-biology/sibsim4/sibsim4-0.14.ebuild b/sci-biology/sibsim4/sibsim4-0.14.ebuild deleted file mode 100644 index 64ada6178..000000000 --- a/sci-biology/sibsim4/sibsim4-0.14.ebuild +++ /dev/null @@ -1,27 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -DESCRIPTION="A rewrite and improvement upon sim4, a DNA-mRNA aligner" -HOMEPAGE="http://sibsim4.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/SIBsim4-${PV}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -IUSE="" -KEYWORDS="~x86" - -DEPEND="" -RDEPEND="" - -S="${WORKDIR}/SIBsim4-${PV}" - -src_unpack() { - unpack ${A} - sed -i 's/CFLAGS = \(.*\)/CFLAGS := \1 ${CFLAGS}/' ${S}/Makefile -} - -src_install() { - dobin SIBsim4 - doman SIBsim4.1 -} diff --git a/sci-biology/sibsim4/sibsim4-0.15.ebuild b/sci-biology/sibsim4/sibsim4-0.15.ebuild deleted file mode 100644 index 64ada6178..000000000 --- a/sci-biology/sibsim4/sibsim4-0.15.ebuild +++ /dev/null @@ -1,27 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -DESCRIPTION="A rewrite and improvement upon sim4, a DNA-mRNA aligner" -HOMEPAGE="http://sibsim4.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/SIBsim4-${PV}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -IUSE="" -KEYWORDS="~x86" - -DEPEND="" -RDEPEND="" - -S="${WORKDIR}/SIBsim4-${PV}" - -src_unpack() { - unpack ${A} - sed -i 's/CFLAGS = \(.*\)/CFLAGS := \1 ${CFLAGS}/' ${S}/Makefile -} - -src_install() { - dobin SIBsim4 - doman SIBsim4.1 -} diff --git a/sci-biology/tgi-tools/ChangeLog b/sci-biology/tgi-tools/ChangeLog deleted file mode 100644 index 9c5619c04..000000000 --- a/sci-biology/tgi-tools/ChangeLog +++ /dev/null @@ -1,20 +0,0 @@ -# ChangeLog for sci-biology/tgi-tools -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +tgi-tools-0.1.ebuild: - Mass import from sunrise - - 15 Apr 2007; Stefan Schweizer <genstef@gentoo.org> tgi-tools-0.1.ebuild: - Remove RESTRICT=mirror, Artistic license allows redistribution - - 14 Dec 2006; Markus Ullmann <jokey@gentoo.org> tgi-tools-0.1.ebuild: - Whiteys - - 12 Dec 2006; Jakub Moc <jakub@gentoo.org> tgi-tools-0.1.ebuild: - QA: quoting, formatting, nomirror -> mirror etc. - - 12 Dec 2006; Andrey Kislyuk (weaver) <weaver@horizon.ath.cx> - +tgi-tools-0.1.ebuild, +metadata.xml: - New ebuild, Bug 157827 - diff --git a/sci-biology/tgi-tools/Manifest b/sci-biology/tgi-tools/Manifest deleted file mode 100644 index 59293b72c..000000000 --- a/sci-biology/tgi-tools/Manifest +++ /dev/null @@ -1,26 +0,0 @@ -DIST cdbfasta.tar.gz 23470 RMD160 d587deaac94eced97728b0596022ea5e6a1bc75e SHA1 c7455ad2ac92cd1ee1293f0100fd871d71e4d630 SHA256 6862061d923f49579568e62be06bf434e79dbb56dfafe573353b4eb7d8ab9c9c -DIST mdust.tar.gz 7526 RMD160 c04a6ba5a56724bfee70b8fe31f0bf4132b74885 SHA1 8885f206d61a76c6623c4115af02793bb52911c4 SHA256 9722806920fc6772dc92f99e7a59554c5f7c35b596dca0df9ed03ff2e5c6440d -DIST nrcl.tar.gz 13151 RMD160 65f2e829fcf2da0134873eaa13098995b4472e15 SHA1 a9bf20a6f0f10201a03fb51644fa64e2519abd84 SHA256 3402a3efb38e3c7320831ca07e228374bbbba34d5b8a161446a7fc0bf4397808 -DIST psx.tar.gz 7797 RMD160 2b6de75126f19cbb60e1ed0b9988a935ad021a45 SHA1 3e0ac61f9ef2e546ff571bfc269e904138b445b9 SHA256 6759f1001be93fcfca9cebd0c764088c4942f2d7feee100d10cf2fbb39e4cd5a -DIST pvmsx.tar.gz 10963 RMD160 1d14cb6e25a533f8a9879b04c5eb9e04532874e5 SHA1 562ea8628e47739ec7b98c622c894fe45e210c98 SHA256 c403534a0d13c2457a50c8ff5e9aeb5979d91a56307478b6420b5caf40e62230 -DIST sclust.tar.gz 14370 RMD160 1334a6a555c6ed3c8ad03ed697887bba76e8441e SHA1 19afe2272cb8b01e631313d57c38cd7fc575fc3c SHA256 4550350993a56d4e5e7163247965d4af91c32cc40ff7e0eeff3a0c6e04fd8ef4 -DIST seqclean.tar.gz 181383 RMD160 d3faae9e342e95dcbd66d39d80eb7e53f0527275 SHA1 8b3871cc0d70d71ff1bc7bfedc3638ff60e4c889 SHA256 4175b6ca7d93a7ea39e6dfb513500205c29a61b393a96bb2a7861a5540fd0d6d -DIST tclust.tar.gz 8864 RMD160 e77a8ce86fa779bbce7c46efbce2245ec7735681 SHA1 35793ddc161c31ce0827073e993f4f6456dbbd35 SHA256 d4f9714f56f77c0e31f0ec9cd9da374899184f40fd688b06292e40412fbb7445 -DIST tgi_cpp_library.tar.gz 58212 RMD160 a85d0e0232a3956f93e521a73075d81d5ecfaaf3 SHA1 1039291f5f0ca617d025bcfacf4f271a3a225001 SHA256 555a81a63233d725868f6179cf3f5d74cceaa040058e2e4ded20f95487c89875 -DIST trimpoly.tar.gz 12562 RMD160 7345812dbbcea3d7fd2018ba1b04254863d171a4 SHA1 3558e9663cba6e6c179ca6f9a019f95d7aa1d4db SHA256 aa8f4a47d45ee534a15edf8e325f341a72d0ce0fa659ccfd8591c15bef44da4f -DIST zmsort.tar.gz 5537 RMD160 cf6599dbd417f5ea50ec41db7909a2415ac28e68 SHA1 27a88033d99da8671fcae598f21e5b8cb7089e40 SHA256 32c5b72e22ae0fbd1784174dcff74e1a40817e29e98b2a0a32a21d83ace6b7fd -EBUILD tgi-tools-0.1.ebuild 1556 RMD160 3a3782fd845e309a5a5cef84a870d7529581f684 SHA1 1fb231c11bf653fd7645380cb0c4fbbeb2478f0a SHA256 d5548b8ea3e0600a731e8bf9b186dd4027bcc7422b0960a17e072041e817d15e -MD5 8c76fb96266f761e7ce56e28e236bfd3 tgi-tools-0.1.ebuild 1556 -RMD160 3a3782fd845e309a5a5cef84a870d7529581f684 tgi-tools-0.1.ebuild 1556 -SHA256 d5548b8ea3e0600a731e8bf9b186dd4027bcc7422b0960a17e072041e817d15e tgi-tools-0.1.ebuild 1556 -MISC ChangeLog 697 RMD160 d873f6a3192e71e8499646192ef725f58987ba96 SHA1 5f916419a43396c3ecd92b93f1ec732ca4f65999 SHA256 2111f501e89d7be9aa417de1aa13d2163740c3b7284d93c07db3924385e5ed57 -MD5 427621e2286227ccc8a41d25fb35aedd ChangeLog 697 -RMD160 d873f6a3192e71e8499646192ef725f58987ba96 ChangeLog 697 -SHA256 2111f501e89d7be9aa417de1aa13d2163740c3b7284d93c07db3924385e5ed57 ChangeLog 697 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 -MD5 1e678929a9fec6632e227bdf2262e9a1 metadata.xml 170 -RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 metadata.xml 170 -SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 metadata.xml 170 -MD5 b74c49cd884b0fc9e4063bbf4f668097 files/digest-tgi-tools-0.1 2402 -RMD160 64d7dc05d77a3600c7db302a0b2fc562ff01c6b6 files/digest-tgi-tools-0.1 2402 -SHA256 228c18a3a616b8bb8c1c977bfe05a5908bc5795380e9886dd7e3d8ed02c5042d files/digest-tgi-tools-0.1 2402 diff --git a/sci-biology/tgi-tools/files/digest-tgi-tools-0.1 b/sci-biology/tgi-tools/files/digest-tgi-tools-0.1 deleted file mode 100644 index 366567bf2..000000000 --- a/sci-biology/tgi-tools/files/digest-tgi-tools-0.1 +++ /dev/null @@ -1,33 +0,0 @@ -MD5 e42d20b19adeafdf4162f32482bce1b0 cdbfasta.tar.gz 23470 -RMD160 d587deaac94eced97728b0596022ea5e6a1bc75e cdbfasta.tar.gz 23470 -SHA256 6862061d923f49579568e62be06bf434e79dbb56dfafe573353b4eb7d8ab9c9c cdbfasta.tar.gz 23470 -MD5 9cd31b3a1647c3e0f955694a57903c0a mdust.tar.gz 7526 -RMD160 c04a6ba5a56724bfee70b8fe31f0bf4132b74885 mdust.tar.gz 7526 -SHA256 9722806920fc6772dc92f99e7a59554c5f7c35b596dca0df9ed03ff2e5c6440d mdust.tar.gz 7526 -MD5 1888e9dc225052b3b9bda1ca9e6b0e03 nrcl.tar.gz 13151 -RMD160 65f2e829fcf2da0134873eaa13098995b4472e15 nrcl.tar.gz 13151 -SHA256 3402a3efb38e3c7320831ca07e228374bbbba34d5b8a161446a7fc0bf4397808 nrcl.tar.gz 13151 -MD5 09e181d2c5e71460164e301a24a055cf psx.tar.gz 7797 -RMD160 2b6de75126f19cbb60e1ed0b9988a935ad021a45 psx.tar.gz 7797 -SHA256 6759f1001be93fcfca9cebd0c764088c4942f2d7feee100d10cf2fbb39e4cd5a psx.tar.gz 7797 -MD5 7350f170008b232c1935de743cc40c4e pvmsx.tar.gz 10963 -RMD160 1d14cb6e25a533f8a9879b04c5eb9e04532874e5 pvmsx.tar.gz 10963 -SHA256 c403534a0d13c2457a50c8ff5e9aeb5979d91a56307478b6420b5caf40e62230 pvmsx.tar.gz 10963 -MD5 a8bc3fb633bf1a3dcd56cbde29352dac sclust.tar.gz 14370 -RMD160 1334a6a555c6ed3c8ad03ed697887bba76e8441e sclust.tar.gz 14370 -SHA256 4550350993a56d4e5e7163247965d4af91c32cc40ff7e0eeff3a0c6e04fd8ef4 sclust.tar.gz 14370 -MD5 ce4a5cc23c6458dd959e0e5dd0cd22ce seqclean.tar.gz 181383 -RMD160 d3faae9e342e95dcbd66d39d80eb7e53f0527275 seqclean.tar.gz 181383 -SHA256 4175b6ca7d93a7ea39e6dfb513500205c29a61b393a96bb2a7861a5540fd0d6d seqclean.tar.gz 181383 -MD5 a0893732e9e427978bf6d460727619a5 tclust.tar.gz 8864 -RMD160 e77a8ce86fa779bbce7c46efbce2245ec7735681 tclust.tar.gz 8864 -SHA256 d4f9714f56f77c0e31f0ec9cd9da374899184f40fd688b06292e40412fbb7445 tclust.tar.gz 8864 -MD5 c568ef74bab896d09c2773b0764d8b31 tgi_cpp_library.tar.gz 58212 -RMD160 a85d0e0232a3956f93e521a73075d81d5ecfaaf3 tgi_cpp_library.tar.gz 58212 -SHA256 555a81a63233d725868f6179cf3f5d74cceaa040058e2e4ded20f95487c89875 tgi_cpp_library.tar.gz 58212 -MD5 dcaee491b6a6765673164acc1158fa3a trimpoly.tar.gz 12562 -RMD160 7345812dbbcea3d7fd2018ba1b04254863d171a4 trimpoly.tar.gz 12562 -SHA256 aa8f4a47d45ee534a15edf8e325f341a72d0ce0fa659ccfd8591c15bef44da4f trimpoly.tar.gz 12562 -MD5 94fd4565d949e140f237d3b2a4c16212 zmsort.tar.gz 5537 -RMD160 cf6599dbd417f5ea50ec41db7909a2415ac28e68 zmsort.tar.gz 5537 -SHA256 32c5b72e22ae0fbd1784174dcff74e1a40817e29e98b2a0a32a21d83ace6b7fd zmsort.tar.gz 5537 diff --git a/sci-biology/tgi-tools/metadata.xml b/sci-biology/tgi-tools/metadata.xml deleted file mode 100644 index 7e3286984..000000000 --- a/sci-biology/tgi-tools/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>maintainer-wanted</herd> -</pkgmetadata> diff --git a/sci-biology/tgi-tools/tgi-tools-0.1.ebuild b/sci-biology/tgi-tools/tgi-tools-0.1.ebuild deleted file mode 100644 index 9a50c4bb3..000000000 --- a/sci-biology/tgi-tools/tgi-tools-0.1.ebuild +++ /dev/null @@ -1,50 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -DESCRIPTION="The Gene Index Project utilities for genomic data processing: seqclean, cdbfasta, psx" -HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/" - -for i in seqclean/{seqclean,mdust,trimpoly} cdbfasta/cdbfasta tgicl/{psx,pvmsx,zmsort,tclust,sclust,nrcl,tgi_cpp_library}; do - SRC_URI="${SRC_URI} ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/${i}.tar.gz" -done - -LICENSE="Artistic" -SLOT="0" -IUSE="pvm" -KEYWORDS="~x86" - -DEPEND="pvm? ( sys-cluster/pvm )" -RDEPEND=${DEPEND} - -S=${WORKDIR} - -src_unpack() { - unpack {seqclean,mdust,trimpoly,cdbfasta,tgi_cpp_library}.tar.gz - for i in nrcl sclust tclust zmsort psx pvmsx; do - mkdir "${S}"/${i} - cd "${S}"/${i} - unpack ${i}.tar.gz - done -} - -src_compile() { - sed -i 's/use Mailer;/#use Mailer;/' ${S}/seqclean/seqclean - sed -i 's/-V\t\tverbose/-V\t\tverbose\\/' ${S}/zmsort/zmsort.cpp - # TODO: fix error in nrcl - for i in cdbfasta mdust psx sclust tclust trimpoly zmsort $(use pvm && echo pvmsx); do - sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' ${S}/${i}/Makefile - cd ${S}/${i} || die "cd ${i} failed" - emake || die "emake failed in ${i}" - done -} - -src_install() { - dobin cdbfasta/{cdbfasta,cdbyank} seqclean/{seqclean,cln2qual,bin/seqclean.psx} - for i in mdust psx sclust tclust trimpoly zmsort $(use pvm && echo pvmsx); do - dobin ${i}/${i} - done - for i in cdbfasta seqclean; do - newdoc ${i}/README README.${i} - done -} diff --git a/sci-biology/tigr-assembler/ChangeLog b/sci-biology/tigr-assembler/ChangeLog deleted file mode 100644 index 8ac88cca5..000000000 --- a/sci-biology/tigr-assembler/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/tigr-assembler -# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> - +tigr-assembler-2.0.ebuild: - Mass import from sunrise - - 19 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +tigr-assembler-2.0.ebuild, - +metadata.xml: - new package (bug 175282) - diff --git a/sci-biology/tigr-assembler/Manifest b/sci-biology/tigr-assembler/Manifest deleted file mode 100644 index 04f274a7e..000000000 --- a/sci-biology/tigr-assembler/Manifest +++ /dev/null @@ -1,16 +0,0 @@ -DIST TIGR_Assembler_v2.tar.gz 3252950 RMD160 5b7eaeebf8791acb3b53ab864f6e9c6571c70877 SHA1 8bd1886eb33d203598ac03decc7798a1fa0d85d7 SHA256 b5b660db388788173f7bd9778fe9b1e904bed7f6a464ab6cc92cd4608e70fd42 -EBUILD tigr-assembler-2.0.ebuild 635 RMD160 d899446e7e35320a8a3023d690c45c58b939e062 SHA1 ed6846be95b4b769205fcfa16dfdb4cd4ddb430c SHA256 75cecd058f71fb26541672c951bfeb6461a4e7f021d635ddc377bc83e8cea25c -MD5 a5fab4210ac95955cd08785622ac6a53 tigr-assembler-2.0.ebuild 635 -RMD160 d899446e7e35320a8a3023d690c45c58b939e062 tigr-assembler-2.0.ebuild 635 -SHA256 75cecd058f71fb26541672c951bfeb6461a4e7f021d635ddc377bc83e8cea25c tigr-assembler-2.0.ebuild 635 -MISC ChangeLog 366 RMD160 456390461b0286ece0f75002dcd49f90bd42e754 SHA1 a6d057fde4a594d8fb2d127bbb443d85ea039d9a SHA256 9b8273b2bfb0bd78ef4656523a6edd6e4fc4d4467c90fdc34995c1f95662c288 -MD5 5fd015ba27ac7f2f4fcaffb0ce3d5ee1 ChangeLog 366 -RMD160 456390461b0286ece0f75002dcd49f90bd42e754 ChangeLog 366 -SHA256 9b8273b2bfb0bd78ef4656523a6edd6e4fc4d4467c90fdc34995c1f95662c288 ChangeLog 366 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 -MD5 1e678929a9fec6632e227bdf2262e9a1 metadata.xml 170 -RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 metadata.xml 170 -SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 metadata.xml 170 -MD5 34ea976ee140a76384b08b8d33f832b0 files/digest-tigr-assembler-2.0 256 -RMD160 88adcd5f128ee53e27bef0bfef88f7e45e11344d files/digest-tigr-assembler-2.0 256 -SHA256 240d7e7304c146d042614059a62e89a5a4911483cba0c8895731f1aadbcffdf2 files/digest-tigr-assembler-2.0 256 diff --git a/sci-biology/tigr-assembler/files/digest-tigr-assembler-2.0 b/sci-biology/tigr-assembler/files/digest-tigr-assembler-2.0 deleted file mode 100644 index 738d485c7..000000000 --- a/sci-biology/tigr-assembler/files/digest-tigr-assembler-2.0 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 70b56f15fc9e44436abf67ca8ba909fa TIGR_Assembler_v2.tar.gz 3252950 -RMD160 5b7eaeebf8791acb3b53ab864f6e9c6571c70877 TIGR_Assembler_v2.tar.gz 3252950 -SHA256 b5b660db388788173f7bd9778fe9b1e904bed7f6a464ab6cc92cd4608e70fd42 TIGR_Assembler_v2.tar.gz 3252950 diff --git a/sci-biology/tigr-assembler/metadata.xml b/sci-biology/tigr-assembler/metadata.xml deleted file mode 100644 index 7e3286984..000000000 --- a/sci-biology/tigr-assembler/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>maintainer-wanted</herd> -</pkgmetadata> diff --git a/sci-biology/tigr-assembler/tigr-assembler-2.0.ebuild b/sci-biology/tigr-assembler/tigr-assembler-2.0.ebuild deleted file mode 100644 index bc42ce0b6..000000000 --- a/sci-biology/tigr-assembler/tigr-assembler-2.0.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -DESCRIPTION="A whole-genome shotgun assembler from TIGR" -HOMEPAGE="http://www.tigr.org/software/assembler/" -SRC_URI="ftp://ftp.tigr.org/pub/software/assembler/TIGR_Assembler_v2.tar.gz" - -LICENSE="Artistic" -SLOT="0" -IUSE="" -KEYWORDS="~x86" - -DEPEND="" -RDEPEND="" - -S="${WORKDIR}/TIGR_Assembler_v2" - -src_compile() { - sed -i 's/CFLAGS.*= -O/CFLAGS := -O ${CFLAGS}/' "${S}/src/Makefile" || die "sed failed" - cd "${S}/src" - emake || die "emake failed" -} - -src_install() { - dobin bin/{run_TA,TIGR_Assembler} - dodoc README -} |