Import from science overlay

Package-Manager: portage-2.2_rc8/cvs/Linux 2.6.26-tuxonice i686

8 files changed, 126 insertions, 0 deletions

diff --git a/sci-biology/glimmer/ChangeLog b/sci-biology/glimmer/ChangeLog
new file mode 100644
index 000000000000..1ff0c293bf76
--- /dev/null
+++ b/sci-biology/glimmer/ChangeLog
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+# ChangeLog for sci-biology/glimmer
+# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v 1.1 2008/09/07 13:06:53 weaver Exp $
+
+*glimmer-3.02 (07 Sep 2008)
+
+  07 Sep 2008; weaver <weaver@gentoo.org> +metadata.xml,
+  +glimmer-3.02.ebuild:
+  Import from science overlay
+
diff --git a/sci-biology/glimmer/Manifest b/sci-biology/glimmer/Manifest
new file mode 100644
index 000000000000..b3566040bbf1
--- /dev/null
+++ b/sci-biology/glimmer/Manifest
@@ -0,0 +1,4 @@
+DIST glimmer302.tar.gz 5637075 RMD160 bc29bb045f7a4179504cb3843741393f42e11ab8 SHA1 e2f27fdab82cd8978f1452bfcd4c0287c52b77b7 SHA256 a1e422ee56f495f9f99e1741ba2043f026fc8182afcc47cb20cfd2d989537221
+EBUILD glimmer-3.02.ebuild 839 RMD160 fbe13a8a0733c0b2c54c94d3ccf7d45d85ce6496 SHA1 272a86bfe05bc0497e942c0935df0296acdbc4fc SHA256 f71989667fdaa9701f56d29cc0eec1645293998b2351ee40ec9255d02006d2d5
+MISC ChangeLog 261 RMD160 3d4b2dad41a2f02e4f2a2e8649db1dc83f1d4291 SHA1 e840f8786b3f1b5a7d9eaf1828e7d080e45d85cc SHA256 c6e746e68cb4436a9fc4f7f17a7fd3e0b4ec80ebaf1b9b4c100c96f71ca20a33
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
diff --git a/sci-biology/glimmer/glimmer-3.02.ebuild b/sci-biology/glimmer/glimmer-3.02.ebuild
new file mode 100644
index 000000000000..d3239d16c2e9
--- /dev/null
+++ b/sci-biology/glimmer/glimmer-3.02.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/glimmer-3.02.ebuild,v 1.1 2008/09/07 13:06:53 weaver Exp $
+
+inherit versionator
+
+MY_PV=$(delete_all_version_separators)
+
+DESCRIPTION="An HMM-based microbial gene finding system from TIGR"
+HOMEPAGE="http://www.cbcb.umd.edu/software/glimmer/"
+SRC_URI="http://www.cbcb.umd.edu/software/${PN}/${PN}${MY_PV}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S=${WORKDIR}/${PN}${PV}
+
+src_compile() {
+	sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \
+		-e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths"
+	cd src
+	emake || die "emake failed"
+}
+
+src_install() {
+	rm bin/test
+	dobin bin/*
+
+	dodir /usr/share/${PN}/scripts
+	insinto /usr/share/${PN}/scripts
+	doins scripts/*
+
+	dodoc glim302notes.pdf
+}
diff --git a/sci-biology/glimmer/metadata.xml b/sci-biology/glimmer/metadata.xml
new file mode 100644
index 000000000000..7e3286984488
--- /dev/null
+++ b/sci-biology/glimmer/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/glimmerhmm/ChangeLog b/sci-biology/glimmerhmm/ChangeLog
new file mode 100644
index 000000000000..2d5f928e70d3
--- /dev/null
+++ b/sci-biology/glimmerhmm/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/glimmerhmm
+# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmerhmm/ChangeLog,v 1.1 2008/09/07 13:11:13 weaver Exp $
+
+*glimmerhmm-3.0.1 (07 Sep 2008)
+
+  07 Sep 2008; weaver <weaver@gentoo.org> +metadata.xml,
+  +glimmerhmm-3.0.1.ebuild:
+  Import from science overlay
+
diff --git a/sci-biology/glimmerhmm/Manifest b/sci-biology/glimmerhmm/Manifest
new file mode 100644
index 000000000000..be271373b012
--- /dev/null
+++ b/sci-biology/glimmerhmm/Manifest
@@ -0,0 +1,4 @@
+DIST GlimmerHMM-3.0.1.tar.gz 45475952 RMD160 273cb74458e3f444cd9f8ca9f6618335aea5465f SHA1 6caf10a3fb79660e48d88560869dee0394961f1a SHA256 c956838a398483003ff1af867c65aca082b82340d8b302b9ada77d1b246954e4
+EBUILD glimmerhmm-3.0.1.ebuild 1256 RMD160 049d1518fd52df807711eb0f1f6ea786b0a28810 SHA1 b2ba513811da89a032bf458d7e59a76a27247259 SHA256 e7b5d7d8552b3815c3494691f09fcbeef3211087947e79a30187a375ca53da2e
+MISC ChangeLog 272 RMD160 9973a96edc8f75ca7d4e6122a7d6d5193b1fab95 SHA1 b0260de4de4510a34c289951d241e1406e3a58d3 SHA256 1524f8b5953a9a63c4223b6aeb5a8734016126346dad13e11386d9ab30d1ef03
+MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild
new file mode 100644
index 000000000000..b8715912c9c2
--- /dev/null
+++ b/sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild,v 1.1 2008/09/07 13:11:13 weaver Exp $
+
+MY_P=GlimmerHMM
+
+DESCRIPTION="An eukaryotic gene finding system from TIGR"
+HOMEPAGE="http://www.cbcb.umd.edu/software/GlimmerHMM/"
+SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/${MY_P}-${PV}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S=${WORKDIR}/${MY_P}
+
+src_compile() {
+	sed -i -e 's|\(my $scriptdir=\)$FindBin::Bin|\1"/usr/share/'${PN}'/training_utils"|' \
+		-e 's|\(use lib\) $FindBin::Bin|\1 "/usr/share/'${PN}'/lib"|' train/trainGlimmerHMM || die "sed failed"
+	sed -i 's/^CFLAGS[ ]*=.*//' */makefile
+
+	cd sources
+	emake || die "emake failed in sources"
+	cd "${S}/train" || die "failed to cd"
+	emake || die "emake failed in train"
+}
+
+src_install() {
+	dobin sources/glimmerhmm train/trainGlimmerHMM
+
+	dodir /usr/share/${PN}/{lib,models,training_utils}
+	insinto /usr/share/${PN}/lib
+	doins train/*.pm
+	insinto /usr/share/${PN}/models
+	doins -r trained_dir/*
+	insinto /usr/share/${PN}/training_utils
+	insopts -m755
+	doins train/{build{1,2,-icm,-icm-noframe},erfapp,falsecomp,findsites,karlin,score,score{2,ATG,ATG2,STOP,STOP2},splicescore}
+
+	dodoc README.first train/readme.train
+}
diff --git a/sci-biology/glimmerhmm/metadata.xml b/sci-biology/glimmerhmm/metadata.xml
new file mode 100644
index 000000000000..3302123e5718
--- /dev/null
+++ b/sci-biology/glimmerhmm/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>