From 56128fa1333a6a68ee12f2a9a79b350f0942d932 Mon Sep 17 00:00:00 2001 From: Andrey Kislyuk Date: Thu, 26 Feb 2009 14:14:35 -0500 Subject: In gentoo-x86 --- sci-biology/repeatmasker-libraries/ChangeLog | 20 -------- sci-biology/repeatmasker-libraries/Manifest | 4 -- sci-biology/repeatmasker-libraries/metadata.xml | 5 -- .../repeatmasker-libraries-20090120.ebuild | 32 ------------- sci-biology/repeatmasker/ChangeLog | 18 -------- sci-biology/repeatmasker/Manifest | 4 -- sci-biology/repeatmasker/metadata.xml | 5 -- sci-biology/repeatmasker/repeatmasker-3.2.7.ebuild | 54 ---------------------- sci-biology/trf/ChangeLog | 7 --- sci-biology/trf/Manifest | 4 -- sci-biology/trf/metadata.xml | 9 ---- sci-biology/trf/trf-4.0.ebuild | 35 -------------- 12 files changed, 197 deletions(-) delete mode 100644 sci-biology/repeatmasker-libraries/ChangeLog delete mode 100644 sci-biology/repeatmasker-libraries/Manifest delete mode 100644 sci-biology/repeatmasker-libraries/metadata.xml delete mode 100644 sci-biology/repeatmasker-libraries/repeatmasker-libraries-20090120.ebuild delete mode 100644 sci-biology/repeatmasker/ChangeLog delete mode 100644 sci-biology/repeatmasker/Manifest delete mode 100644 sci-biology/repeatmasker/metadata.xml delete mode 100644 sci-biology/repeatmasker/repeatmasker-3.2.7.ebuild delete mode 100644 sci-biology/trf/ChangeLog delete mode 100644 sci-biology/trf/Manifest delete mode 100644 sci-biology/trf/metadata.xml delete mode 100644 sci-biology/trf/trf-4.0.ebuild diff --git a/sci-biology/repeatmasker-libraries/ChangeLog b/sci-biology/repeatmasker-libraries/ChangeLog deleted file mode 100644 index 91a79b00a..000000000 --- a/sci-biology/repeatmasker-libraries/ChangeLog +++ /dev/null @@ -1,20 +0,0 @@ -# ChangeLog for sci-biology/repeatmasker-libraries -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 19 Feb 2009; weaver ChangeLog: - Version bump - - 08 Jul 2008; weaver - -repeatmasker-libraries-20061006.ebuild, - +repeatmasker-libraries-20080611.ebuild: - Version bump - - 27 Apr 2007; Andrey Kislyuk - +repeatmasker-libraries-20061006.ebuild: - Mass import from sunrise - - 20 Apr 2007; Andrey Kislyuk - +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 01889a8cb..000000000 --- a/sci-biology/repeatmasker-libraries/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -DIST repeatmaskerlibraries-20090120.tar.gz 10113533 RMD160 b18cd4002dcd7f14e64a34bbca5343b3e27effde SHA1 1741d80cb57115cec1f866f3e0d2ce06c497c98c SHA256 77924ffb0e8e2a30d421b11ad23c89ec4661feaa87d5138af971796a4543663a -EBUILD repeatmasker-libraries-20090120.ebuild 739 RMD160 8086701394a16377d1e33cac42eb6b99d2ac6aaf SHA1 d193741dd47dc146820e06d5c4e5aa4a85f27676 SHA256 4da31d956af1481118dbb5569ddabc8ba32e88027ea444e0fdbc74786421a8aa -MISC ChangeLog 613 RMD160 d458084f0d40740b258ad300c0bf3b5c375b7593 SHA1 85f42e1ad476558981456014c667ff69de9ac3cc SHA256 547d34bf5bee4cb2382cbdd1f75a5035a46df83d7189bbd4fd8b9915354f9130 -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 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 @@ - - - -maintainer-wanted - diff --git a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20090120.ebuild b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20090120.ebuild deleted file mode 100644 index 9ceb9a55c..000000000 --- a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20090120.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2009 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-${PV}.tar.gz" - -LICENSE="as-is" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="" - -S="${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 1469a7f4f..000000000 --- a/sci-biology/repeatmasker/ChangeLog +++ /dev/null @@ -1,18 +0,0 @@ -# ChangeLog for sci-biology/repeatmasker -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 19 Feb 2009; weaver ChangeLog: - Version bump - - 08 Jul 2008; weaver +repeatmasker-3.2.5.ebuild: - Version bump - - 27 Apr 2007; Andrey Kislyuk - +repeatmasker-3.1.7.ebuild: - Mass import from sunrise - - 20 Apr 2007; Andrey Kislyuk +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 14f962ed4..000000000 --- a/sci-biology/repeatmasker/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -DIST RepeatMasker-open-3-2-7.tar.gz 11398018 RMD160 63a79ea9146805cc1e7f4cca8b94903136bf2a0c SHA1 22ca2ea2369e1543d58c82954870e114e25c80b9 SHA256 3ceb21658f23780c345d27bb603ef407b953c59dce5b97436a578d28dcb7e477 -EBUILD repeatmasker-3.2.7.ebuild 1453 RMD160 dfb1948d89508ab02c7235258d58ccf7c904bb6c SHA1 714e1365a2bd6890594123404445a1a3947ef8da SHA256 2ae89968c5d164fc7ba0beead789fbe78e2aed5c1563a203c6df8458e82db345 -MISC ChangeLog 519 RMD160 cf1d63d7fbf4f1244c6985834a120f83087ad703 SHA1 1375aea6055760632945de921defc239432b5cab SHA256 8b993fe2e6b5dba88249b76fc444bb33550096d8dbeb7c58eed9d37ebdf7b55a -MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 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 @@ - - - -maintainer-wanted - 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 f98859159..000000000 --- a/sci-biology/repeatmasker/repeatmasker-3.2.7.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2009 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="~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}'|' \ - "${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die -} - -src_install() { - dobin DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask - - dodir /usr/share/${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/trf/ChangeLog b/sci-biology/trf/ChangeLog deleted file mode 100644 index bb539ea24..000000000 --- a/sci-biology/trf/ChangeLog +++ /dev/null @@ -1,7 +0,0 @@ -# ChangeLog for sci-biology/trf -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 19 Feb 2009; weaver ChangeLog: - New package sci-biology/trf, ebuild written by me - diff --git a/sci-biology/trf/Manifest b/sci-biology/trf/Manifest deleted file mode 100644 index 0cd12929a..000000000 --- a/sci-biology/trf/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -DIST trf400.linux.exe 87767 RMD160 de28ff3dd895c285bcb76a045625a10490ca6d26 SHA1 9f6de58cb050cc7b80b794aa10aeb7072913514b SHA256 903f408f56666ab193a1ad001785d1d1db9d068f78b56ce1ff09a9805d6cf6d5 -EBUILD trf-4.0.ebuild 837 RMD160 decdbe8298801672e43d1c9cd09610a0e3758367 SHA1 1d49450a60f7f621080bf4c66eb01ce027a3f60a SHA256 cb64add492029facbb182ebb3d76a5b5d2a1b8593198f40605f07162f7f61fba -MISC ChangeLog 222 RMD160 959b61e86f184d9306806f44f6601f848cbb7ece SHA1 36ed796d2b3a9146647aee3d97116d198d9bdad9 SHA256 255ee50b0c54e58ae505ad99516a8879572a57c05634a3742203df6bb498f3fe -MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 diff --git a/sci-biology/trf/metadata.xml b/sci-biology/trf/metadata.xml deleted file mode 100644 index 3302123e5..000000000 --- a/sci-biology/trf/metadata.xml +++ /dev/null @@ -1,9 +0,0 @@ - - - - - weaver@gentoo.org - Andrey Kislyuk - - sci-biology - diff --git a/sci-biology/trf/trf-4.0.ebuild b/sci-biology/trf/trf-4.0.ebuild deleted file mode 100644 index 377b9e1e3..000000000 --- a/sci-biology/trf/trf-4.0.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit eutils - -DESCRIPTION="Tandem Repeats Finder" -HOMEPAGE="http://tandem.bu.edu/trf/trf.html" -SRC_URI="http://tandem.bu.edu/trf/downloads/trf400.linux.exe" - -LICENSE="as-is" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -DEPEND="" -RDEPEND="" -# gtk? ( x11-libs/gtk+ ) x11-libs/pango[X] - -S="${WORKDIR}" - -src_unpack() { - cp "${DISTDIR}/trf400.linux.exe" "${S}" -} - -src_install() { - exeinto /opt/${PN} - doexe trf400.linux.exe || die - dosym /opt/${PN}/trf400.linux.exe /usr/bin/trf || die - # GTK version (http://tandem.bu.edu/trf/downloads/trf400.linuxgtk.exe) has broken linking - #if use gtk; then - # doexe trf400.linuxgtk.exe || die - # make_desktop_entry /opt/${PN}/trf400.linuxgtk.exe "Tandem Repeats Finder" || die - #fi -} -- cgit v1.2.3-65-gdbad