diff options
author | Justin Lecher <jlec@gentoo.org> | 2013-06-16 22:18:52 +0200 |
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committer | Justin Lecher <jlec@gentoo.org> | 2013-06-16 22:18:52 +0200 |
commit | e1e48799c623338fedab433347c64dfce9b9aebe (patch) | |
tree | 2484eba8fb9a58e4dd06979c036ba570c55c9f9d | |
parent | Merge branch 'ercpe' (diff) | |
parent | sci-biology/twinscan: Bump to EAPI=5 and fix license (diff) | |
download | sci-e1e48799c623338fedab433347c64dfce9b9aebe.tar.gz sci-e1e48799c623338fedab433347c64dfce9b9aebe.tar.bz2 sci-e1e48799c623338fedab433347c64dfce9b9aebe.zip |
Merge branch 'fixing'
* fixing:
sci-biology/twinscan: Bump to EAPI=5 and fix license
sci-biology/ssaha2-bin: Version Bump; restrict license; add QA_PREBUILT for binaries
sci-biology/smalt-bin: Version Bump; restrict license; add QA_PREBUILT for binaries
sci-biology/sequin: Version BUmp; restrcit license; add QA_PREBUILT for binaries; install html files into sys path
sci-biology/quicktree: Bump to EAPI=5 and fix license
sci-biology/gap2caf: Bump to EAPI=5 and fix license; make it build with eautoreconf
sci-biology/erpin: Bump to EAPI=5 and respect FLAGS / AR
sci-biology/clover: Version BUmp; fixed license; respect LDFLAGS
34 files changed, 292 insertions, 215 deletions
diff --git a/sci-biology/clover/ChangeLog b/sci-biology/clover/ChangeLog index 18775e4df..edcb8dd7d 100644 --- a/sci-biology/clover/ChangeLog +++ b/sci-biology/clover/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/clover -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -clover-2010.02.19.ebuild, + +clover-2011.10.24.ebuild, metadata.xml: + Version BUmp; fixed license; respect LDFLAGS + *clover-2010.02.19 (23 Aug 2010) 23 Aug 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> diff --git a/sci-biology/clover/Manifest b/sci-biology/clover/Manifest index 701b84d6e..4a3827eb9 100644 --- a/sci-biology/clover/Manifest +++ b/sci-biology/clover/Manifest @@ -1,2 +1,2 @@ -DIST clover-2010-02-19.tar.gz 15641 SHA256 f6de99b9ce5676af8b4179e12c4701f81f0b17ac5dadacfe7affa38ad2a585f5 -DIST jaspar2005core 14913 SHA256 498a560c67411789106b50ccdfd9bc41f571d77c2fe9bfba7e95128c0a122fe4 +DIST clover-2011-10-24.tar.gz 15843 SHA256 52ba95c118a32e6ea1097f356dfb0277be4464b834285f65eaaebcf8f504a93e SHA512 edf773943a33d58b07b7a47ca9e6c0fe08715d7f445ef1283848a14eb72d084b2113a911f23bc484b3229ec14b8eeb50d460c6b9fef89db2fa031ea059b36b93 WHIRLPOOL 785c7273c10bc6e4261e91a9dae224ff595aad3f033fb03edbe403d8cb97b456c0fe285e1a537bde3508e5e4a8f2ea5aa442fb3cb72640464df2a24da8be0ae0 +DIST jaspar2009core 54400 SHA256 a76cd1462e7b9c38f64e2049593d21fa90479b968c7997ca3d83f8489327b981 SHA512 621eac23fb0db78391d3d51471f03eccc791e1b348b23b5d9dae32b082c8301e847ee1eea4a76ac188796b639125a0970e5f0b3c0d3c673ae6f6634856c980a0 WHIRLPOOL c148ee32894ec1bd55a4665fd516eb82e6e5904e6a74bb6248d70ef7fef1a1376888a6fe53bcd959faeb8665b7c2bda3668f6801ed2e07c2c445a241a1ebcc4d diff --git a/sci-biology/clover/clover-2010.02.19.ebuild b/sci-biology/clover/clover-2010.02.19.ebuild deleted file mode 100644 index 239cc30e4..000000000 --- a/sci-biology/clover/clover-2010.02.19.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit toolchain-funcs versionator - -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}-${MY_PV}.tar.gz http://zlab.bu.edu/clover/jaspar2005core" - -LICENSE="as-is" -SLOT="0" -IUSE="" -KEYWORDS="~x86 ~amd64" - -DEPEND="" -RDEPEND="" - -S="${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/clover-2011.10.24.ebuild b/sci-biology/clover/clover-2011.10.24.ebuild new file mode 100644 index 000000000..cfb057432 --- /dev/null +++ b/sci-biology/clover/clover-2011.10.24.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit toolchain-funcs versionator + +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}-${MY_PV}.tar.gz + http://zlab.bu.edu/clover/jaspar2009core" + +LICENSE="freedist" +SLOT="0" +IUSE="" +KEYWORDS="~x86 ~amd64" + +S="${WORKDIR}/${PN}-${MY_PV}" + +src_prepare() { + sed \ + -e "s:g++:$(tc-getCXX) \$(LDFLAGS):; s:-Wall -O3:${CFLAGS}:" \ + -i Makefile || die "sed failed" +} + +src_install() { + dobin clover + insinto /usr/share/${PN} + doins "${DISTDIR}/jaspar2009core" +} + +pkg_postinst() { + einfo "The motif library jaspar2009core has been installed in" + einfo " /usr/share/clover/jaspar2009core" + einfo "You can pass this library to clover for motif search, or use your own library." +} diff --git a/sci-biology/clover/metadata.xml b/sci-biology/clover/metadata.xml index 622c9ed81..fd501d278 100644 --- a/sci-biology/clover/metadata.xml +++ b/sci-biology/clover/metadata.xml @@ -1,6 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-biology</herd> -<maintainer><email>maintainer-wanted@gentoo.org</email></maintainer> + <herd>sci-biology</herd> + <maintainer> + <email>maintainer-wanted@gentoo.org</email> + </maintainer> </pkgmetadata> diff --git a/sci-biology/erpin/ChangeLog b/sci-biology/erpin/ChangeLog index f98fe95cc..de94a4865 100644 --- a/sci-biology/erpin/ChangeLog +++ b/sci-biology/erpin/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/erpin -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> erpin-5.5b.ebuild, metadata.xml: + Bump to EAPI=5 and respect FLAGS / AR + 23 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: New package, ebuild written by me diff --git a/sci-biology/erpin/Manifest b/sci-biology/erpin/Manifest index a5845e4ac..0c7cd75e4 100644 --- a/sci-biology/erpin/Manifest +++ b/sci-biology/erpin/Manifest @@ -1,2 +1,2 @@ -DIST ErpinBatch.1.4.tar.gz 2195075 SHA256 5da4c69d88092e79f4f5d73e7d67dfccbb3d4a8cbe38c74169548ef608f25808 -DIST erpin5.5b.serv.tar.gz 1145698 SHA256 0433ed25dd54491ddc4c025bb61d78d36797c2c83c61f260b5663c44cbad4d4d +DIST ErpinBatch.1.4.tar.gz 2195075 SHA256 5da4c69d88092e79f4f5d73e7d67dfccbb3d4a8cbe38c74169548ef608f25808 SHA512 1fe33a0760e843c1f2096e5fa923275d2109e10ba42ff18d24898d59de7d2e31ae2adee915d35d1afc1b1f41dee1243986878bc6440223a0def372fd0536c261 WHIRLPOOL 82871a1836d3cbe7a271e31ed15a2e2aca29a06262105bf1dd03a7bb64e6167a6dedd6bd56c4832c11579d3ca307706b7493d1b81e5cd2b63c166a74cb7577c2 +DIST erpin5.5b.serv.tar.gz 1145698 SHA256 0433ed25dd54491ddc4c025bb61d78d36797c2c83c61f260b5663c44cbad4d4d SHA512 f6ca25e72e26d98b609b54984bf74e4bdc0ff239e94e7f8851b303022b7399bcdf879589827e2c35763b8547487740832d51b9997a6a230d8f24b4c506d338e5 WHIRLPOOL 188ab1e408bec9a4d484b476aa73cce7acdc340f5c1cd5c31bdce8c511b0864abd0312feb815ae0d28b75de99c0225bb8d4765dd9d584295af37b998f9abfc53 diff --git a/sci-biology/erpin/erpin-5.5b.ebuild b/sci-biology/erpin/erpin-5.5b.ebuild index 8aafe2078..3673a3225 100644 --- a/sci-biology/erpin/erpin-5.5b.ebuild +++ b/sci-biology/erpin/erpin-5.5b.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/bowtie/bowtie-0.10.1.ebuild,v 1.3 2009/09/22 11:43:28 maekke Exp $ -EAPI="2" +EAPI=5 inherit toolchain-funcs @@ -10,10 +10,11 @@ ERPIN_BATCH_V=1.4 DESCRIPTION="Easy RNA Profile IdentificatioN, an RNA motif search program" HOMEPAGE="http://tagc.univ-mrs.fr/erpin/" -SRC_URI="http://rna.igmors.u-psud.fr/download/Erpin/erpin${PV}.serv.tar.gz +SRC_URI=" + http://rna.igmors.u-psud.fr/download/Erpin/erpin${PV}.serv.tar.gz http://rna.igmors.u-psud.fr/download/Erpin/ErpinBatch.${ERPIN_BATCH_V}.tar.gz" -LICENSE="as-is" +LICENSE="all-rights-reserved" SLOT="0" IUSE="" KEYWORDS="~amd64 ~x86" @@ -29,19 +30,21 @@ src_prepare() { find -name '*.mk' | xargs sed -i \ -e 's/strip $@/echo skipping strip $@/' \ -e '/CFLAGS =/ d' \ - -e "s/CC = .*/CC = $(tc-getCC)/" || die + -e "s/CC = .*/CC = $(tc-getCC)/" \ + -e "s: -o : ${LDFLAGS} -o :g" \ + -e "s:ar :$(tc-getAR) :g" || die sed -i 's/cc -O2/$(tc-getCC) ${CFLAGS}/' erpin${PV}.serv/sum/sum.mk || die } src_compile() { - emake -C erpin${PV}.serv -f erpin.mk || die + emake -C erpin${PV}.serv -f erpin.mk } src_install() { - dobin erpin${PV}.serv/bin/* || die + dobin erpin${PV}.serv/bin/* insinto /usr/share/${PN} - doins -r erpin${PV}.serv/scripts ErpinBatch.${ERPIN_BATCH_V} || die + doins -r erpin${PV}.serv/scripts ErpinBatch.${ERPIN_BATCH_V} exeinto /usr/share/${PN} - newexe "${FILESDIR}/erpincommand-${PV}.pl" erpincommand.pl || die - dodoc erpin${PV}.serv/doc/doc*.pdf || die + newexe "${FILESDIR}/erpincommand-${PV}.pl" erpincommand + dodoc erpin${PV}.serv/doc/doc*.pdf } diff --git a/sci-biology/erpin/metadata.xml b/sci-biology/erpin/metadata.xml index 3302123e5..fc7c76942 100644 --- a/sci-biology/erpin/metadata.xml +++ b/sci-biology/erpin/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer> - <email>weaver@gentoo.org</email> - <name>Andrey Kislyuk</name> - </maintainer> - <herd>sci-biology</herd> + <maintainer> + <email>weaver@gentoo.org</email> + <name>Andrey Kislyuk</name> + </maintainer> + <herd>sci-biology</herd> </pkgmetadata> diff --git a/sci-biology/gap2caf/ChangeLog b/sci-biology/gap2caf/ChangeLog new file mode 100644 index 000000000..8e35f8604 --- /dev/null +++ b/sci-biology/gap2caf/ChangeLog @@ -0,0 +1,8 @@ +# ChangeLog for sci-biology/gap2caf +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> gap2caf-2.1.0.ebuild, + metadata.xml: + Bump to EAPI=5 and fix license; make it build with eautoreconf + diff --git a/sci-biology/gap2caf/Manifest b/sci-biology/gap2caf/Manifest index 3dbd5c548..7d17476c0 100644 --- a/sci-biology/gap2caf/Manifest +++ b/sci-biology/gap2caf/Manifest @@ -1,2 +1,2 @@ -DIST gap2caf-2.1.0.tar.gz 92905 SHA256 1fd237cf1e83c3c4c3b67d2d35c9f059cc7eda9f6ac7886fab994e2386283b9a -DIST staden-2.0.0b8.tar.gz 4312143 SHA256 c13aa0c22dcac6b10d13501dcb630efad51d7c171968e0bb30113667b49cfa9d +DIST gap2caf-2.1.0.tar.gz 92905 SHA256 1fd237cf1e83c3c4c3b67d2d35c9f059cc7eda9f6ac7886fab994e2386283b9a SHA512 2a843d861b7be6d656793f4876953596b91a93c3da7d23ee8edc10c4620e33fc96a16beaeaaf4f66c1f5c5084eb8a9a255d4fa8e1ca6e87e96372f2459167c90 WHIRLPOOL f5a3360de7c6b8741e5e85a9bc25198de4dbcbebdee73ba48a7e1460eb4d778648a5c93f0bb44c10e15a4fa46dd0c741fc10c8e33ae8c50e2c7cd9914a56aa81 +DIST staden-2.0.0b8.tar.gz 4312143 SHA256 c13aa0c22dcac6b10d13501dcb630efad51d7c171968e0bb30113667b49cfa9d SHA512 ddd273d281557595c90b93304cd03205adbe1367845ef43763a8c75d06c2729d99ca8622439ff5c31217595481a9ac4ccedf87c5948821aeaeb73c96133dc411 WHIRLPOOL f086f7f81884091a34c9933a2bb901146eefcd2dc4cb4b940228de3a51daee4c1f9d5613ca34ec345bcce48fc53bed6c4a408f5b5d6e87ac5c4deda222daee24 diff --git a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild index 861bbc8f0..ca12aedf2 100644 --- a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild +++ b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild @@ -1,26 +1,25 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=5 inherit autotools eutils DESCRIPTION="GAP4 file format to CAF v2 format converter for genomic assembly data" HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/" -SRC_URI="ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/gap2caf-2.1.0.tar.gz - http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz" +SRC_URI=" + ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/gap2caf-2.1.0.tar.gz + http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz" -LICENSE="as-is staden" +LICENSE="GRL staden" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND="" -RDEPEND="${DEPEND}" - -DEPEND="sci-biology/staden - >=dev-lang/tcl-8.5" +DEPEND=" + sci-biology/staden + >=dev-lang/tcl-8.5" RDEPEND="${DEPEND}" #src_prepare(){ @@ -29,13 +28,14 @@ RDEPEND="${DEPEND}" src_prepare(){ sed -i 's:/include/tcl8.4:/include:' configure.ac || die - sed -i 's:libtcl8.4:libtcl8.5:' configure.ac || die - sed -i 's:tcl8.4:tcl8.5:' src/Makefile.am || die - eaclocal - eautomake - eautoconf - sed -i 's:/include/tcl8.4:/include:' configure - sed -i 's:libtcl8.4:libtcl8.5:' configure + sed -i 's:libtcl8.4:libtcl:' configure.ac || die + sed \ + -e 's:tcl8.4:tcl:' \ + -e 's:pkglib_PROGRAMS:pkglibexec_PROGRAMS:g' \ + -i src/Makefile.am || die + eautoreconf + sed -i 's:/include/tcl8.4:/include:' configure || die + sed -i 's:libtcl8.4:libtcl:' configure || die } src_configure(){ @@ -45,12 +45,13 @@ src_configure(){ #LDFLAGS="$LDFLAGS -L/usr/lib/staden -lmutlib -lprimer3 -lg -lmisc" \ # STADENROOT=/usr/share/staden \ # STADENSRC="${WORKDIR}"/staden-2.0.0b8-src \ - econf --with-stadenroot=/usr \ - --with-tcl=/usr \ - --with-stadensrc="${WORKDIR}"/staden-2.0.0b8-src || die + econf \ + --with-stadenroot=/usr \ + --with-tcl=/usr \ + --with-stadensrc="${WORKDIR}"/staden-2.0.0b8-src #sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' Makefile || die #sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' src/Makefile || die - sed -i 's:tcl8.4:tcl8.5:' src/Makefile || die + sed -i 's:tcl8.4:tcl:' src/Makefile || die # The below tricks in overall do not help, only for -ltk_utils somehow sed -i 's:-ltk_utils:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -ltk_utils -rpath-link:' src/Makefile || die @@ -68,7 +69,7 @@ src_install(){ # # Instead, we rely on sci-biology/staden providind /etc/env.d/99staden file providing LDPATH=/usr/lib/staden dobin src/gap2caf - dodoc README || die + dodoc README } # BUG #259848 diff --git a/sci-biology/gap2caf/metadata.xml b/sci-biology/gap2caf/metadata.xml index 07b525505..2bc893037 100644 --- a/sci-biology/gap2caf/metadata.xml +++ b/sci-biology/gap2caf/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-biology</herd> - <maintainer> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> </pkgmetadata> diff --git a/sci-biology/quicktree/ChangeLog b/sci-biology/quicktree/ChangeLog index ba6206456..00e62e40d 100644 --- a/sci-biology/quicktree/ChangeLog +++ b/sci-biology/quicktree/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/quicktree -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> quicktree-1.1-r1.ebuild, + metadata.xml: + Bump to EAPI=5 and fix license + *quicktree-1.1-r1 (08 Nov 2010) 08 Nov 2010; Kacper Kowalik <xarthisius@gentoo.org> -quicktree-1.1.ebuild, diff --git a/sci-biology/quicktree/Manifest b/sci-biology/quicktree/Manifest index 3bb33a29d..acb09d64c 100644 --- a/sci-biology/quicktree/Manifest +++ b/sci-biology/quicktree/Manifest @@ -1 +1 @@ -DIST quicktree-1.1.tar.gz 39035 SHA256 3b5986a8d7b8e59ad5cdc30bd7c7d91431909c25230e8fed13494f21337da6ef +DIST quicktree-1.1.tar.gz 39035 SHA256 3b5986a8d7b8e59ad5cdc30bd7c7d91431909c25230e8fed13494f21337da6ef SHA512 1b58b786a5f0c96d7a86280e0349eb48b9a1f11160e0266e6b837dfde20a159de1393ec46bc4cdcaae09ffa59c68e8bbc5a985286133b67d6ab8fa6e248823fb WHIRLPOOL 0837a98f78f2ac56ed1f19d89a6e6fa632de4946d3a8b2fe8ec58347e58cf0cc1bcf52dbfaf63bcbc29a3994dc0f3fb61c447e0dbe4711c00201a5ac8a4b9ae7 diff --git a/sci-biology/quicktree/metadata.xml b/sci-biology/quicktree/metadata.xml index 3302123e5..fc7c76942 100644 --- a/sci-biology/quicktree/metadata.xml +++ b/sci-biology/quicktree/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer> - <email>weaver@gentoo.org</email> - <name>Andrey Kislyuk</name> - </maintainer> - <herd>sci-biology</herd> + <maintainer> + <email>weaver@gentoo.org</email> + <name>Andrey Kislyuk</name> + </maintainer> + <herd>sci-biology</herd> </pkgmetadata> diff --git a/sci-biology/quicktree/quicktree-1.1-r1.ebuild b/sci-biology/quicktree/quicktree-1.1-r1.ebuild index 99053dc6f..e32314f97 100644 --- a/sci-biology/quicktree/quicktree-1.1-r1.ebuild +++ b/sci-biology/quicktree/quicktree-1.1-r1.ebuild @@ -1,6 +1,6 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasttree/fasttree-2.0.1.ebuild,v 1.1 2009/09/10 23:14:22 weaver Exp $ +# $Header: $ EAPI=2 @@ -8,9 +8,9 @@ inherit toolchain-funcs DESCRIPTION="Rapid reconstruction of phylogenies by the Neighbor-Joining method" HOMEPAGE="http://www.sanger.ac.uk/Software/analysis/quicktree/" -SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/quicktree/quicktree.tar.gz -> quicktree-${PV}.tar.gz" +SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/${PN}/${PN}.tar.gz -> ${P}.tar.gz" -LICENSE="as-is" +LICENSE="GRL" SLOT="0" IUSE="" KEYWORDS="~amd64 ~x86" @@ -18,15 +18,16 @@ KEYWORDS="~amd64 ~x86" S=${WORKDIR}/${PN}_${PV} src_prepare() { - sed -e "s/\-O2 \-Wall/${CFLAGS}/" \ + sed \ + -e "s/\-O2 \-Wall/${CFLAGS}/" \ -i Makefile || die } src_compile() { - emake CC="$(tc-getCC)" LFLAGS="${LDFLAGS}" || die + emake CC="$(tc-getCC)" LFLAGS="${LDFLAGS}" } src_install() { - dobin bin/quicktree || die - dodoc README || die + dobin bin/quicktree + dodoc README } diff --git a/sci-biology/sequin/ChangeLog b/sci-biology/sequin/ChangeLog index ca9c2b059..639b7c7a9 100644 --- a/sci-biology/sequin/ChangeLog +++ b/sci-biology/sequin/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-biology/sequin -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*sequin-20121202 (16 Jun 2013) + + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -sequin-20090722.ebuild, + +sequin-20121202.ebuild: + Version BUmp; restrcit license; add QA_PREBUILT for binaries; install html + files into sys path + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: Fixed herd entry in metadata.xml diff --git a/sci-biology/sequin/Manifest b/sci-biology/sequin/Manifest index 442d7db82..956270595 100644 --- a/sci-biology/sequin/Manifest +++ b/sci-biology/sequin/Manifest @@ -1,2 +1,2 @@ -DIST sequin-20090722-x86.tar.gz 5999782 SHA256 f12fe7fa084a1d19a75e67cfcb4027cefb91c819b7c6219499072a87f00bdc51 -DIST sequin-20090722-x86_64.tar.gz 6911415 SHA256 338de057edf9c14e911f69c372c9480675c2b5a4b24efed605dcbdf7e8e4d486 +DIST sequin-20121202-x86.tar.gz 6760477 SHA256 a07bb9ad491b1ef0c7f03381bd73cab4bb6305a0897c117b071ad5a633a4a95e SHA512 a93d79b5a7ed7a42cc02107a0ca87051e3f95554afb103ad9fb17d1c98d4f0f5b3f01b512f63b8902cc9865a38eb10cf65cbae46a2fcf0ed4a9c1b9b697f47e9 WHIRLPOOL 288d75b4426edb9d657fe727a484a8f6009c71eff6f3202b412bbc635f52613f89955120ad0170c18f5e7d4bbf6e7f81a06b2f4b9b7f5166dc97617ee8a1c682 +DIST sequin-20121202-x86_64.tar.gz 8277570 SHA256 fe7d430a32320f22917fa515c3ba13b6fb3c9af42916759a353b9b62c0437b81 SHA512 33664d49cb0b33194d64781086ee27fad65602b6c058c4cc079ce840b6a4774c675b21c82bfcf2648b6b1f95fb0bcacc4f2eddb25d06fb8a363d4993cbb20b32 WHIRLPOOL 3f5c107701755eab1021014f9e9b333a74af42f49a1c6595d15cc38100ba1d5fe4c91fe1eef31083f937aae9bac66d94f21cd253430d1bb68e341ceb7308797b diff --git a/sci-biology/sequin/sequin-20090722.ebuild b/sci-biology/sequin/sequin-20090722.ebuild deleted file mode 100644 index b1d419648..000000000 --- a/sci-biology/sequin/sequin-20090722.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw/clustalw-2.0.12.ebuild,v 1.1 2009/10/18 21:14:11 weaver Exp $ - -EAPI=2 - -inherit eutils - -DESCRIPTION="A tool to facilitate submission of data to the GenBank, EMBL, and DDBJ sequence databases" -HOMEPAGE="http://www.ncbi.nlm.nih.gov/Sequin/" -SRC_URI="amd64? ( ftp://ftp.ncbi.nih.gov/sequin/old/${PV}/sequin.linux-x86_64.tar.gz -> ${P}-x86_64.tar.gz ) - x86? ( ftp://ftp.ncbi.nih.gov/sequin/old/${PV}/sequin.linux-x86.tar.gz -> ${P}-x86.tar.gz )" - -LICENSE="as-is" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="x11-libs/libXmu - x11-libs/libXp" - -S="${WORKDIR}" - -src_install() { - insinto /opt/${PN} - doins -r * || die - exeinto /opt/${PN} - doexe sequin || die - dosym /opt/${PN}/sequin /usr/bin/sequin || die - make_desktop_entry sequin Sequin || die -} diff --git a/sci-biology/sequin/sequin-20121202.ebuild b/sci-biology/sequin/sequin-20121202.ebuild new file mode 100644 index 000000000..5e586dcd8 --- /dev/null +++ b/sci-biology/sequin/sequin-20121202.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw/clustalw-2.0.12.ebuild,v 1.1 2009/10/18 21:14:11 weaver Exp $ + +EAPI=5 + +inherit eutils + +DESCRIPTION="A tool to facilitate submission of data to the GenBank, EMBL, and DDBJ sequence databases" +HOMEPAGE="http://www.ncbi.nlm.nih.gov/Sequin/" +SRC_URI=" + amd64? ( ftp://ftp.ncbi.nih.gov/sequin/sequin.linux-x86_64.tar.gz -> ${P}-x86_64.tar.gz ) + x86? ( ftp://ftp.ncbi.nih.gov/sequin/sequin.linux.tar.gz -> ${P}-x86.tar.gz )" +# amd64? ( ftp://ftp.ncbi.nih.gov/sequin/old/${PV}/sequin.linux-x86_64.tar.gz -> ${P}-x86_64.tar.gz ) +# x86? ( ftp://ftp.ncbi.nih.gov/sequin/old/${PV}/sequin.linux-x86.tar.gz -> ${P}-x86.tar.gz )" + +LICENSE="all-rights-reserved" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND=" + x11-libs/libXmu + x11-libs/libXp" + +S="${WORKDIR}" + +QA_PREBUILT="/opt/.*" + +src_install() { + dohtml -r *htm images + rm -rf *htm images || die + + insinto /opt/${PN} + doins -r * + + exeinto /opt/${PN} + doexe sequin + + dosym /opt/${PN}/sequin /opt/bin/sequin + + make_desktop_entry sequin Sequin +} diff --git a/sci-biology/smalt-bin/ChangeLog b/sci-biology/smalt-bin/ChangeLog index f3268fd32..7f6f91f99 100644 --- a/sci-biology/smalt-bin/ChangeLog +++ b/sci-biology/smalt-bin/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-biology/smalt-bin -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*smalt-bin-0.7.4 (16 Jun 2013) + + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -smalt-bin-0.5.1.ebuild, + +smalt-bin-0.7.4.ebuild, metadata.xml: + Version Bump; restrict license; add QA_PREBUILT for binaries + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> smalt-bin-0.5.1.ebuild: Cleaned ebuild and fixed LICENSE diff --git a/sci-biology/smalt-bin/Manifest b/sci-biology/smalt-bin/Manifest index f9f5194ab..0e8053bb2 100644 --- a/sci-biology/smalt-bin/Manifest +++ b/sci-biology/smalt-bin/Manifest @@ -1 +1 @@ -DIST smalt-0.5.1.tgz 534824 SHA256 c8bca18a7ded7ad4b7070be7478bd046cf2d6a0a81054dfd96ebdba65c0a49d0 +DIST smalt-0.7.4.tgz 1437480 SHA256 a6997fcbef746c57f889c3784b2bc9c399ad03562ed8d4a835180ba8cc6822fe SHA512 9c31f358ef4094566bdc67f92b2576e6cf15a010bbf7dc1eb4a66afb2107253dfe4947a529c10c579484ccd7aff6aaae048ea8b17fd468804b08d88fb6588e39 WHIRLPOOL 65c1a52608d26e3411a77137fa03c65ae30cc845d5e9f676ab4c1a53812f1fcbd2300b4e5a0a8839c24c00f526f0a5627b6facbec54cbe86af7d132857b728c1 diff --git a/sci-biology/smalt-bin/metadata.xml b/sci-biology/smalt-bin/metadata.xml index 07b525505..2bc893037 100644 --- a/sci-biology/smalt-bin/metadata.xml +++ b/sci-biology/smalt-bin/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-biology</herd> - <maintainer> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> </pkgmetadata> diff --git a/sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild b/sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild deleted file mode 100644 index 7566c2097..000000000 --- a/sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=4 - -DESCRIPTION="Pairwise sequence alignment mapping DNA reads onto genomic reference, better over SSAHA2" -HOMEPAGE="http://www.sanger.ac.uk/resources/software/smalt/" -SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-"${PV}".tgz" - -LICENSE="as-is" -SLOT="0" -KEYWORDS="~x86 ~amd64" -IUSE="" - -S="${WORKDIR}"/smalt-"${PV}" - -src_install(){ - use x86 && newbin smalt_i386 smalt - use amd64 && newbin smalt_x86_64 smalt - use ia64 && newbin smalt_ia64 - - dodoc NEWS smalt_manual.pdf - doman smalt.1 -} diff --git a/sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild b/sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild new file mode 100644 index 000000000..01acc05a9 --- /dev/null +++ b/sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +MY_PN="${PN%-bin}" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Pairwise sequence alignment mapping DNA reads onto genomic reference, better over SSAHA2" +HOMEPAGE="http://www.sanger.ac.uk/resources/software/smalt/" +SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/${MY_PN}/${MY_P}.tgz" + +LICENSE="all-rights-reserved" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +S="${WORKDIR}"/${MY_P} + +QA_PREBUILT="/opt/.*" + +src_install(){ + exeinto /opt/bin + use x86 && newexe ${MY_PN}_i386 ${MY_PN} + use amd64 && newexe ${MY_PN}_x86_64 ${MY_PN} + use ia64 && newexe ${MY_PN}_ia64 ${MY_PN} + + dodoc NEWS ${MY_PN}_manual.pdf + doman ${MY_PN}.1 +} diff --git a/sci-biology/ssaha2-bin/ChangeLog b/sci-biology/ssaha2-bin/ChangeLog index 914725e6e..8b3f2ffef 100644 --- a/sci-biology/ssaha2-bin/ChangeLog +++ b/sci-biology/ssaha2-bin/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/ssaha2-bin -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -ssaha2-bin-2.5.3.ebuild, + +ssaha2-bin-2.5.5.ebuild, metadata.xml: + Version Bump; restrict license; add QA_PREBUILT for binaries + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> ssaha2-bin-2.5.3.ebuild: Cleaned ebuild and fixed LICENSE diff --git a/sci-biology/ssaha2-bin/Manifest b/sci-biology/ssaha2-bin/Manifest index 3cd3275a6..f1a6a5db5 100644 --- a/sci-biology/ssaha2-bin/Manifest +++ b/sci-biology/ssaha2-bin/Manifest @@ -1,5 +1,4 @@ -DIST samflag.c 2424 SHA256 945958214ef1adc40029a6b3c323c37338e095e9e2bcbff5e5ec05aadbdb67d0 -DIST ssaha2-manual.pdf 163188 SHA256 1a0529168b71ac55e13b34264a854daa6a5dac9468f81ccb5b63bd5e1baafdbf -DIST ssaha2_i686.tgz 288481 SHA256 7d173d763d9f685ef3d0075124bf8b763c6d2d3ed1a1f823bc66d6b6b029abed -DIST ssaha2_ia64.tgz 458507 SHA256 3eb2a31559911f3ee87e11f3b977962da31b60c25ea0c9a064edfd1165b6b5dd -DIST ssaha2_x86_64.tgz 287790 SHA256 0135ab2e285a898d450744b7c9d643efbeb6048783169a6647f310ce2e7b8138 +DIST samflag.c 2424 SHA256 945958214ef1adc40029a6b3c323c37338e095e9e2bcbff5e5ec05aadbdb67d0 SHA512 50ef4d134e5fab4f1399fd2eb35de0c8ce901c23e360a52ee5cdca117c124c77f432a50a666d655dc0f04089db84d873f9251e68ff6f6f4ac327e23362657aa7 WHIRLPOOL c89abd1bac315aaadfc4456c4ec4252a6ccdd1f42db604b60568d3ee7e367f8ec99ff7915aeaac7dafa594bd29bb11affb3f62ed9d6dd577dd407c2c4c93e7c5 +DIST ssaha2-manual.pdf 163188 SHA256 1a0529168b71ac55e13b34264a854daa6a5dac9468f81ccb5b63bd5e1baafdbf SHA512 2a43d038684519d3a4e1fca54b75ac731961dc1e9e1034914eff481b303e5b49d11f4d9149e56a6e06292107f5be3ee6357bb9ec508cdb4de1fac677fade5d0e WHIRLPOOL 25040635acf63d874c453d5e2c2bb93dd2f44537c79ce5d3109bd59a345cbf41e4106b05039a8d3e0b00a8e1bd7a66d923161b8f0fe2544f10c37f5a4bfbbaf9 +DIST ssaha2_v2.5.5_i686.tgz 1045230 SHA256 b66ddbf1374cbcf583ff5413cb7c17dd0e63c2372d227c26526fa79597cb39c8 SHA512 e5611a2b382348e84b7cc40496b42d78ca1b5a5d641acfdb1371bff79dbe055f8c22db10b3a428d7943a6824246141e28e71146722a613585d82034187d81e32 WHIRLPOOL 169d316e548a4cc223755534b235163f0356129b6aab44540cbe5eb6083ea46f47ee689097301ecc86974da8a7b21f5887db8e88b772668c3049de31120581de +DIST ssaha2_v2.5.5_x86_64.tgz 1167987 SHA256 478bdbda9d5fe36278748e571299f5eaf39d5172758cf0d0a85fa750f84667d4 SHA512 483dc726e1ac52020481a5721e0ac870fccdec22d9f7e74bddc76cbb76bd10ceccba57ecab9e2787045cde0e6cb74186bd3769e5c7222eb15e9c445ba7ac2592 WHIRLPOOL dbde27ca5e2eeba1c44fc59cd66f1ac6c6fa52647174c184521cf88b9ae8b05633f2fc1bc93b3be6e07e499832ec0938c4fab1017e53706b51c78060f6590b01 diff --git a/sci-biology/ssaha2-bin/metadata.xml b/sci-biology/ssaha2-bin/metadata.xml index 07b525505..2bc893037 100644 --- a/sci-biology/ssaha2-bin/metadata.xml +++ b/sci-biology/ssaha2-bin/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-biology</herd> - <maintainer> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> </pkgmetadata> diff --git a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild index 34b63dd43..96a183dc7 100644 --- a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild +++ b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild @@ -1,34 +1,40 @@ -# Copyright 1999-2011 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 inherit toolchain-funcs +MY_PN="${PN%-bin}" +MY_P="${MY_PN}_v${PV}" + DESCRIPTION="SSAHA2: Sequence Search and Alignment by Hashing Algorithm" HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2" SRC_URI=" - x86? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_i686.tgz ) - amd64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_x86_64.tgz ) - ia64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_ia64.tgz ) + x86? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/${MY_PN}/${MY_P}_i686.tgz ) + amd64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/${MY_PN}/${MY_P}_x86_64.tgz ) ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/samflag.c ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2-manual.pdf" -LICENSE="as-is" +LICENSE="all-rights-reserved" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -use x86 && S="${WORKDIR}"/ssaha2_v"${PV}"_i686 -use amd64 && S="${WORKDIR}"/ssaha2_v"${PV}"_x86_64 -use ia64 && S="${WORKDIR}"/ssaha2_v"${PV}"_ia64 +QA_PREBUILT="/opt/.*" +pkg_setup() { + use x86 && export S="${WORKDIR}"/${MY_P}_i686 + use amd64 && export S="${WORKDIR}"/${MY_P}_x86_64 +} src_compile() { $(tc-getCC) ${CFLAGS} ${LDFLAGS} -o samflag "${DISTDIR}"/samflag.c || die "Failed to compile samflags" } src_install() { - dobin samflag ssaha2 ssaha2Build ssahaSNP + dobin samflag + exeinto /opt/bin + doexe ssaha2 ssaha2Build ssahaSNP dodoc README "${DISTDIR}"/ssaha2-manual.pdf } diff --git a/sci-biology/twinscan/ChangeLog b/sci-biology/twinscan/ChangeLog index 3914a6070..fedf86e90 100644 --- a/sci-biology/twinscan/ChangeLog +++ b/sci-biology/twinscan/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/twinscan -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> twinscan-4.1.2.ebuild, + metadata.xml: + Bump to EAPI=5 and fix license + 07 Mar 2011; Justin Lecher <jlec@gentoo.org> twinscan-4.1.2.ebuild: Correct Slots for gtk 3 introduction to tree diff --git a/sci-biology/twinscan/Manifest b/sci-biology/twinscan/Manifest index e9fea6590..7e7f3adc1 100644 --- a/sci-biology/twinscan/Manifest +++ b/sci-biology/twinscan/Manifest @@ -1 +1 @@ -DIST iscan-4.1.2.tar_.gz 5894833 SHA256 30c7e980b2ccbba22a5e2d7ff0d7c1aaeb610cc1cec81432bb30e87f03f7e56a +DIST twinscan-4.1.2.tar.gz 5894833 SHA256 30c7e980b2ccbba22a5e2d7ff0d7c1aaeb610cc1cec81432bb30e87f03f7e56a SHA512 d216f790f6d0f35a070575d1aa4b5e1866c00132168b381b9177b076b1b2a16f2ecd7a88aa443d7ba6b8f62c3ec2595ba33c4608a674e09d94e9f7dc6a181327 WHIRLPOOL e95df100f970c6cabf9b21a9a6651dcd249fccbfafc908a8766bf26ad5108c08b5de105c5142492bb7b0c13f39bd65836a92be9161cfbbb303147f925e775d99 diff --git a/sci-biology/twinscan/metadata.xml b/sci-biology/twinscan/metadata.xml index 3302123e5..fc7c76942 100644 --- a/sci-biology/twinscan/metadata.xml +++ b/sci-biology/twinscan/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer> - <email>weaver@gentoo.org</email> - <name>Andrey Kislyuk</name> - </maintainer> - <herd>sci-biology</herd> + <maintainer> + <email>weaver@gentoo.org</email> + <name>Andrey Kislyuk</name> + </maintainer> + <herd>sci-biology</herd> </pkgmetadata> diff --git a/sci-biology/twinscan/twinscan-4.1.2.ebuild b/sci-biology/twinscan/twinscan-4.1.2.ebuild index 96b1a049c..516aec88c 100644 --- a/sci-biology/twinscan/twinscan-4.1.2.ebuild +++ b/sci-biology/twinscan/twinscan-4.1.2.ebuild @@ -1,14 +1,16 @@ -# Copyright 1999-2011 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=2 +EAPI=5 + +inherit toolchain-funcs DESCRIPTION="TwinScan, N-SCAN, and Pairagon: A gene structure prediction pipeline" HOMEPAGE="http://mblab.wustl.edu/software/twinscan" -SRC_URI="http://mblab.wustl.edu/software/download/iscan-${PV}.tar_.gz" +SRC_URI="http://mblab.wustl.edu/software/download/iscan-${PV}.tar_.gz -> ${P}.tar.gz" -LICENSE="as-is" +LICENSE="all-rights-reserved" SLOT="0" IUSE="" KEYWORDS="~amd64 ~x86" @@ -18,14 +20,21 @@ RDEPEND="${DEPEND}" S="${WORKDIR}/N-SCAN" -src_unpack() { - unpack ${A} - tar -C "${WORKDIR}" -xf iscan-${PV}.tar_ -} - src_prepare() { sed -i "1 a use lib '/usr/share/${PN}/lib/perl5';" "${S}"/bin/*.pl || die - sed -i '/my $blast_param/ s/#//' "${S}/bin/runTwinscan2.pl" + sed -i '/my $blast_param/ s/#//' "${S}/bin/runTwinscan2.pl" || die + tc-export CC AR RANLIB + + sed \ + -e 's:ar :$(AR) :g' \ + -e 's:ranlib :$(RANLIB) :g' \ + -e 's: -o : $(LDFLAGS) -o :g' \ + -i Makefile || die + + sed \ + -e "/^GLIB_CFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --cflags glib-2.0) -DHAS_GLIB:g" \ + -e "/^GLIB_LFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --libs glib-2.0)-DHAS_GLIB:g" \ + -i Makefile.include || die } src_install() { @@ -35,5 +44,6 @@ src_install() { doins -r "${S}/lib" || die echo "TWINSCAN=/usr" > "${S}"/99${PN} doenvd "${S}"/99${PN} || die + rm -rf examples/tmp dodoc examples/* README* } |