Import from Science overlay

Package-Manager: portage-2.2_rc20/cvs/Linux 2.6.26-gentoo-r4 x86_64

7 files changed, 124 insertions, 0 deletions

diff --git a/sci-biology/repeatmasker-libraries/ChangeLog b/sci-biology/repeatmasker-libraries/ChangeLog
new file mode 100644
index 000000000000..2df0cc200570
--- /dev/null
+++ b/sci-biology/repeatmasker-libraries/ChangeLog
@@ -0,0 +1,26 @@
+# ChangeLog for sci-biology/repeatmasker-libraries
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/repeatmasker-libraries/ChangeLog,v 1.1 2009/02/27 00:12:51 weaver Exp $
+
+*repeatmasker-libraries-20090120 (26 Feb 2009)
+
+  26 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml,
+  +repeatmasker-libraries-20090120.ebuild:
+  Import from Science overlay
+
+  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/metadata.xml b/sci-biology/repeatmasker-libraries/metadata.xml
new file mode 100644
index 000000000000..7e3286984488
--- /dev/null
+++ b/sci-biology/repeatmasker-libraries/metadata.xml
@@ -0,0 +1,5 @@
+<?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
new file mode 100644
index 000000000000..5e9d37f5b75f
--- /dev/null
+++ b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20090120.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20090120.ebuild,v 1.1 2009/02/27 00:12:51 weaver Exp $
+
+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/Manifest b/sci-biology/repeatmasker/Manifest
new file mode 100644
index 000000000000..16d4df08b289
--- /dev/null
+++ b/sci-biology/repeatmasker/Manifest
@@ -0,0 +1,4 @@
+DIST RepeatMasker-open-3-2-7.tar.gz 11398018 RMD160 63a79ea9146805cc1e7f4cca8b94903136bf2a0c SHA1 22ca2ea2369e1543d58c82954870e114e25c80b9 SHA256 3ceb21658f23780c345d27bb603ef407b953c59dce5b97436a578d28dcb7e477
+EBUILD repeatmasker-3.2.7.ebuild 1565 RMD160 4e4025dc55b2f1267a9c69fd1bb68dffe8f860e4 SHA1 fe3f519521e98aafa4443da564f3df6f2591377a SHA256 011c25e9f1f3685a9096b4ea51d511491512f1643206d962e6dfad54f03eea5a
+MISC ChangeLog 788 RMD160 ad1fe4ff6c288710d80efd7d1a7ecf047b4fc95d SHA1 cefe2014e85e4a449fb15d7194267ad6fd292c5a SHA256 428691c9febde6456c143c098deacf44797fb6a72366000200739af2df82d9c0
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
diff --git a/sci-biology/trf/ChangeLog b/sci-biology/trf/ChangeLog
new file mode 100644
index 000000000000..a7d6de7aa342
--- /dev/null
+++ b/sci-biology/trf/ChangeLog
@@ -0,0 +1,13 @@
+# ChangeLog for sci-biology/trf
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/trf/ChangeLog,v 1.1 2009/02/27 00:11:33 weaver Exp $
+
+*trf-4.0 (26 Feb 2009)
+
+  26 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml,
+  +trf-4.0.ebuild:
+  Import from Science overlay
+
+  19 Feb 2009; weaver <weaver@gentoo.org> ChangeLog:
+  New package sci-biology/trf, ebuild written by me
+
diff --git a/sci-biology/trf/metadata.xml b/sci-biology/trf/metadata.xml
new file mode 100644
index 000000000000..3302123e5718
--- /dev/null
+++ b/sci-biology/trf/metadata.xml
@@ -0,0 +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>
+</pkgmetadata>
diff --git a/sci-biology/trf/trf-4.0.ebuild b/sci-biology/trf/trf-4.0.ebuild
new file mode 100644
index 000000000000..a76010b6257a
--- /dev/null
+++ b/sci-biology/trf/trf-4.0.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/trf/trf-4.0.ebuild,v 1.1 2009/02/27 00:11:33 weaver Exp $
+
+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
+}