From 80e1db5f06f3d916c57745b18df3f34e7d84e115 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Thu, 7 Mar 2013 14:53:29 +0000 Subject: sci-biology/repeatmasker: Version BUmp; cleaned old Package-Manager: portage-2.2.0_alpha166/cvs/Linux x86_64 Manifest-Sign-Key: 0x70EB7916 --- sci-biology/repeatmasker/ChangeLog | 11 +++- sci-biology/repeatmasker/Manifest | 22 +++++--- sci-biology/repeatmasker/metadata.xml | 10 ++-- sci-biology/repeatmasker/repeatmasker-3.2.7.ebuild | 58 --------------------- sci-biology/repeatmasker/repeatmasker-3.2.8.ebuild | 58 --------------------- sci-biology/repeatmasker/repeatmasker-3.2.9.ebuild | 58 --------------------- sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild | 59 ++++++++++++++++++++++ 7 files changed, 87 insertions(+), 189 deletions(-) delete mode 100644 sci-biology/repeatmasker/repeatmasker-3.2.7.ebuild delete mode 100644 sci-biology/repeatmasker/repeatmasker-3.2.8.ebuild delete mode 100644 sci-biology/repeatmasker/repeatmasker-3.2.9.ebuild create mode 100644 sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild (limited to 'sci-biology/repeatmasker') diff --git a/sci-biology/repeatmasker/ChangeLog b/sci-biology/repeatmasker/ChangeLog index 350da2366896..a6c5baf3f6e9 100644 --- a/sci-biology/repeatmasker/ChangeLog +++ b/sci-biology/repeatmasker/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-biology/repeatmasker -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/repeatmasker/ChangeLog,v 1.5 2011/02/03 01:34:28 weaver Exp $ +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/repeatmasker/ChangeLog,v 1.6 2013/03/07 14:53:28 jlec Exp $ + +*repeatmasker-4.0.1 (07 Mar 2013) + + 07 Mar 2013; Justin Lecher -repeatmasker-3.2.7.ebuild, + -repeatmasker-3.2.8.ebuild, -repeatmasker-3.2.9.ebuild, + +repeatmasker-4.0.1.ebuild, metadata.xml: + Version BUmp; cleaned old *repeatmasker-3.2.9 (03 Feb 2011) diff --git a/sci-biology/repeatmasker/Manifest b/sci-biology/repeatmasker/Manifest index 783ffd119e36..374510324fbd 100644 --- a/sci-biology/repeatmasker/Manifest +++ b/sci-biology/repeatmasker/Manifest @@ -1,8 +1,14 @@ -DIST RepeatMasker-open-3-2-7.tar.gz 11398018 RMD160 63a79ea9146805cc1e7f4cca8b94903136bf2a0c SHA1 22ca2ea2369e1543d58c82954870e114e25c80b9 SHA256 3ceb21658f23780c345d27bb603ef407b953c59dce5b97436a578d28dcb7e477 -DIST RepeatMasker-open-3-2-8.tar.gz 14096137 RMD160 0f8b463bc9d0d8ac71c0d9261ed7161bcaac63f9 SHA1 76684c1fa85049c5c124df718a08d4d21ab684fe SHA256 644c705db9ec239e9a372d0a262548a4a84b58738775f1427021bdbef90a21c1 -DIST RepeatMasker-open-3-2-9.tar.gz 14123559 RMD160 219cb2c2668346d51ddc7c03f63e24064e84968a SHA1 a8df75da847ea64afec2c2f5fcab915d383c7e45 SHA256 60597ac511f2ad37200b80a69c29a4bccfbc7fe697a6400ce19cb6af83dc71d2 -EBUILD repeatmasker-3.2.7.ebuild 1655 RMD160 f36843903117759852420d27c3b75918846df3ff SHA1 a10f55d589c0abf4f106a346623a8565da44752e SHA256 aa304e8c744fb8f875a0804b8b2ca5d492ffb140a100f1bade7e6da42b6c0c09 -EBUILD repeatmasker-3.2.8.ebuild 1655 RMD160 d08c4b1f921bf8026d04af062227c99fbd9c4bc5 SHA1 3995ebad225693aa83f6744ee346555f25c4f950 SHA256 73bc60d01f51809b2bc5ad3186a434b711ccf19bb7fe1a10b73767152873c185 -EBUILD repeatmasker-3.2.9.ebuild 1665 RMD160 2eecf7a2e1e08cc91102620c457d54f41d75446f SHA1 d9243084592bdcce6656febee2f4fe1328514d28 SHA256 a7ca538a466a473444f0f9f180760d4317a3f259d653e8608294823883c21e91 -MISC ChangeLog 1285 RMD160 41cc016eda4f3900dc369eb9ea993ea77455cab2 SHA1 05602ae50f63e50b3efae96ecbb1ccf79403fbff SHA256 590374ed56ca5f2d87606fa383e17acb428230b8e3efde4497e8a10cb9d51a47 -MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +DIST RepeatMasker-open-4-0-1.tar.gz 84077910 SHA256 638ed02d970052ecb7dac6c71d2cb9625b0a0713df88d46ae78865aa4fd3fc92 SHA512 6b710a02b2964bca6acb25cc918bd56f7caba7b80b3b683972f0584180bf0fd3704f657d7ee341187a4ac86d9883e62eb4f09da237fa8ef1b481137d1a89963e WHIRLPOOL f2d67ea6e97a0667ac9ce89f8ed8c590b911d9cd4fc4482bdc48c0ea7ca07161a8bec267ed3e2a950f6d8c501f992ceadc62e1211a80b6bc1c90d293cbf45e77 +EBUILD repeatmasker-4.0.1.ebuild 1652 SHA256 1a901a3e599eb5651fd95045c2e2674b2aba70db365b0fbc1910789e23978fbf SHA512 6ae68d0d0e82770981bbdc45dc4f296732f18fa2b5306f76a4726042c52b79571ebca64088938f2b205e474bf4c9ee3dd0b7a01e753595dc1385d90ef38b98e7 WHIRLPOOL e4e6619f777f94573349664555eed35706f5138db569928176d6dfdbad90fc32274ae76926033da8af56f614857562e27527147484a1108d216f479b5d5283af +MISC ChangeLog 1524 SHA256 bfb4ece008080da4dfb20e836e28a7780097116e61372918d5d3e79ffff9dbb2 SHA512 cb5d5242572991f4ef6112c27670d733ec9fd002d7e3f5fdc2cf8fd3e984e4131c35fb4fb825e3215aa994692745f269d839bb04fb83da65b8dffa16406ba04f WHIRLPOOL 2ae75f380f64b224f55af44b21fc1590f8377c50093a1910cd5c9cb831d991aa73452cc06a0ddd8aee279d1dd05781e889e21c4f55d9f1a46344ae02025766fa +MISC metadata.xml 266 SHA256 98c7d1da8a728a1f1d796a79d51f25e4164e24048ec1aacbbf0ae2ffb171ff35 SHA512 879cdcca092d4c82b8c63672c91e08e7b01e81419d2c7c7b766de96ba2a32dd1e21c18968ed7172eec8604f52c92b19a31773f428bce9461d9b8190384680194 WHIRLPOOL 0f46288ab7090ad3da5b31816792427e4ad1a950e39a503bb406ebe8789cffedd9c85b46bfbf040fffb8aad443f512c28716a0a6436d0c06309155277060cdcd +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.19 (GNU/Linux) + +iEYEAREIAAYFAlE4qekACgkQgAnW8HDreRY1BQCgnt0eVyYZnOybr65VY2zlbh+c +ztsAoJEukVIbHSUxi2RxbQrfcObRc9sC +=vlhl +-----END PGP SIGNATURE----- diff --git a/sci-biology/repeatmasker/metadata.xml b/sci-biology/repeatmasker/metadata.xml index 3302123e5718..fc7c76942a10 100644 --- a/sci-biology/repeatmasker/metadata.xml +++ b/sci-biology/repeatmasker/metadata.xml @@ -1,9 +1,9 @@ - - weaver@gentoo.org - Andrey Kislyuk - - sci-biology + + weaver@gentoo.org + Andrey Kislyuk + + sci-biology diff --git a/sci-biology/repeatmasker/repeatmasker-3.2.7.ebuild b/sci-biology/repeatmasker/repeatmasker-3.2.7.ebuild deleted file mode 100644 index 9ae733e288f8..000000000000 --- a/sci-biology/repeatmasker/repeatmasker-3.2.7.ebuild +++ /dev/null @@ -1,58 +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/repeatmasker/repeatmasker-3.2.7.ebuild,v 1.2 2009/08/17 19:41:31 weaver Exp $ - -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="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="sci-biology/phrap - sci-biology/trf - >=sci-biology/repeatmasker-libraries-20090120" - -S="${WORKDIR}/RepeatMasker" - -src_compile() { - sed -i -e 's/system( "clear" );//' \ - -e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|' "${S}/configure" || die - echo " -env -/usr/share/${PN} -/usr/bin -1 -/usr/bin -Y -4" | "${S}/configure" || die "configure failed" - sed -i -e 's|use lib $FindBin::RealBin;|use lib "/usr/share/'${PN}'/lib";|' \ - -e 's|".*\(taxonomy.dat\)"|"/usr/share/'${PN}'/\1"|' \ - -e '/$REPEATMASKER_DIR/ s|$FindBin::RealBin|/usr/share/'${PN}'|' \ - "${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die -} - -src_install() { - exeinto /usr/share/${PN} - for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do - doexe $i - dosym /usr/share/${PN}/$i /usr/bin/$i - done - - dodir /usr/share/${PN}/lib - insinto /usr/share/${PN}/lib - doins "${S}"/*.pm - - insinto /usr/share/${PN} - doins -r util Matrices Libraries taxonomy.dat - keepdir /usr/share/${PN}/Libraries - - dodoc README INSTALL *.help -} diff --git a/sci-biology/repeatmasker/repeatmasker-3.2.8.ebuild b/sci-biology/repeatmasker/repeatmasker-3.2.8.ebuild deleted file mode 100644 index e92b1e77e6b3..000000000000 --- a/sci-biology/repeatmasker/repeatmasker-3.2.8.ebuild +++ /dev/null @@ -1,58 +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/repeatmasker/repeatmasker-3.2.8.ebuild,v 1.1 2009/08/20 13:41:10 weaver Exp $ - -EAPI="2" - -MY_PV=${PV//\./-} - -DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA" -HOMEPAGE="http://repeatmasker.org/" -SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz" - -LICENSE="OSL-2.1" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="sci-biology/phrap - sci-biology/trf - >=sci-biology/repeatmasker-libraries-20090604" - -S="${WORKDIR}/RepeatMasker" - -src_configure() { - sed -i -e 's/system( "clear" );//' \ - -e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|' "${S}/configure" || die - echo " -env -/usr/share/${PN} -/usr/bin -1 -/usr/bin -Y -4" | "${S}/configure" || die "configure failed" - sed -i -e 's|use lib $FindBin::RealBin;|use lib "/usr/share/'${PN}'/lib";|' \ - -e 's|".*\(taxonomy.dat\)"|"/usr/share/'${PN}'/\1"|' \ - -e '/$REPEATMASKER_DIR/ s|$FindBin::RealBin|/usr/share/'${PN}'|' \ - "${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die -} - -src_install() { - exeinto /usr/share/${PN} - for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do - doexe $i || die - dosym /usr/share/${PN}/$i /usr/bin/$i || die - done - - dodir /usr/share/${PN}/lib - insinto /usr/share/${PN}/lib - doins "${S}"/*.pm || die - - insinto /usr/share/${PN} - doins -r util Matrices Libraries taxonomy.dat *.help || die - keepdir /usr/share/${PN}/Libraries - - dodoc README INSTALL *.help -} diff --git a/sci-biology/repeatmasker/repeatmasker-3.2.9.ebuild b/sci-biology/repeatmasker/repeatmasker-3.2.9.ebuild deleted file mode 100644 index 4b333576eced..000000000000 --- a/sci-biology/repeatmasker/repeatmasker-3.2.9.ebuild +++ /dev/null @@ -1,58 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/repeatmasker/repeatmasker-3.2.9.ebuild,v 1.1 2011/02/03 01:34:28 weaver Exp $ - -EAPI="2" - -MY_PV=${PV//\./-} - -DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA" -HOMEPAGE="http://repeatmasker.org/" -SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz" - -LICENSE="OSL-2.1" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="sci-biology/rmblast - sci-biology/trf - >=sci-biology/repeatmasker-libraries-20090604" - -S="${WORKDIR}/RepeatMasker" - -src_configure() { - sed -i -e 's/system( "clear" );//' \ - -e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|' "${S}/configure" || die - echo " -env -/usr/share/${PN} -/usr/bin -2 -/opt/rmblast/bin -Y -5" | "${S}/configure" || die "configure failed" - sed -i -e 's|use lib $FindBin::RealBin;|use lib "/usr/share/'${PN}'/lib";|' \ - -e 's|".*\(taxonomy.dat\)"|"/usr/share/'${PN}'/\1"|' \ - -e '/$REPEATMASKER_DIR/ s|$FindBin::RealBin|/usr/share/'${PN}'|' \ - "${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die -} - -src_install() { - exeinto /usr/share/${PN} - for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do - doexe $i || die - dosym /usr/share/${PN}/$i /usr/bin/$i || die - done - - dodir /usr/share/${PN}/lib - insinto /usr/share/${PN}/lib - doins "${S}"/*.pm || die - - insinto /usr/share/${PN} - doins -r util Matrices Libraries taxonomy.dat *.help || die - keepdir /usr/share/${PN}/Libraries - - dodoc README INSTALL *.help -} diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild new file mode 100644 index 000000000000..7b65ee6fc74a --- /dev/null +++ b/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild,v 1.1 2013/03/07 14:53:28 jlec Exp $ + +EAPI=5 + +MY_PV=${PV//\./-} + +DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA" +HOMEPAGE="http://repeatmasker.org/" +SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz" + +LICENSE="OSL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND=" + sci-biology/rmblast + sci-biology/trf + sci-biology/repeatmasker-libraries" + +S="${WORKDIR}/RepeatMasker" + +src_configure() { + sed -i -e 's/system( "clear" );//' \ + -e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|' "${S}/configure" || die + echo " +env +/usr/share/${PN} +/usr/bin +2 +/opt/rmblast/bin +Y +5" | "${S}/configure" || die "configure failed" + sed -i -e 's|use lib $FindBin::RealBin;|use lib "/usr/share/'${PN}'/lib";|' \ + -e 's|".*\(taxonomy.dat\)"|"/usr/share/'${PN}'/\1"|' \ + -e '/$REPEATMASKER_DIR/ s|$FindBin::RealBin|/usr/share/'${PN}'|' \ + "${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die +} + +src_install() { + exeinto /usr/share/${PN} + for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do + doexe $i || die + dosym /usr/share/${PN}/$i /usr/bin/$i || die + done + + dodir /usr/share/${PN}/lib + insinto /usr/share/${PN}/lib + doins "${S}"/*.pm || die + + insinto /usr/share/${PN} + doins -r util Matrices Libraries taxonomy.dat *.help || die + keepdir /usr/share/${PN}/Libraries + + dodoc README INSTALL *.help +} -- cgit v1.2.3-65-gdbad