In gentoo-x86

12 files changed, 0 insertions, 197 deletions

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 <weaver@gentoo.org> ChangeLog:
-  Version bump
-
-  08 Jul 2008; weaver <weaver@gentoo.org>
-  -repeatmasker-libraries-20061006.ebuild,
-  +repeatmasker-libraries-20080611.ebuild:
-  Version bump
-
-  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 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 @@
-<?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-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 <weaver@gentoo.org> ChangeLog:
-  Version bump
-
-  08 Jul 2008; weaver <weaver@gentoo.org> +repeatmasker-3.2.5.ebuild:
-  Version bump
-
-  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 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 @@
-<?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-3.2.7.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 <weaver@gentoo.org> 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 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer>
-		<email>weaver@gentoo.org</email>
-		<name>Andrey Kislyuk</name>
-	</maintainer>
-	<herd>sci-biology</herd>
-</pkgmetadata>
diff --git a/sci-biology/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
-}