sci-biology/glimmerhmm: new package sci-biology/glimmerhmm (bug 170964)

svn path=/sunrise/; revision=3237

5 files changed, 77 insertions, 0 deletions

diff --git a/sci-biology/glimmerhmm/ChangeLog b/sci-biology/glimmerhmm/ChangeLog
new file mode 100644
index 000000000..74099a37c
--- /dev/null
+++ b/sci-biology/glimmerhmm/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-biology/glimmerhmm
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  14 Mar 2007; AK <gentoo@horizon.ath.cx> +glimmerhmm-3.0.1.ebuild,
+  +metadata.xml:
+  new package sci-biology/glimmerhmm (bug 170964)
+
diff --git a/sci-biology/glimmerhmm/Manifest b/sci-biology/glimmerhmm/Manifest
new file mode 100644
index 000000000..94559a80c
--- /dev/null
+++ b/sci-biology/glimmerhmm/Manifest
@@ -0,0 +1,16 @@
+DIST GlimmerHMM-3.0.1.tar.gz 45475952 RMD160 273cb74458e3f444cd9f8ca9f6618335aea5465f SHA1 6caf10a3fb79660e48d88560869dee0394961f1a SHA256 c956838a398483003ff1af867c65aca082b82340d8b302b9ada77d1b246954e4
+EBUILD glimmerhmm-3.0.1.ebuild 1255 RMD160 c8a41f2df4afd845a4009f9e1d00dc13285a787f SHA1 c64815213d631bc33b8bc07261d48b6463bd1bfa SHA256 0c6606de8d1fd3b700391a5fdb002afad6b2df84b0f8aea038ded9d016d96381
+MD5 c64cdc5fd5b16ae3d3cc138303411ed8 glimmerhmm-3.0.1.ebuild 1255
+RMD160 c8a41f2df4afd845a4009f9e1d00dc13285a787f glimmerhmm-3.0.1.ebuild 1255
+SHA256 0c6606de8d1fd3b700391a5fdb002afad6b2df84b0f8aea038ded9d016d96381 glimmerhmm-3.0.1.ebuild 1255
+MISC ChangeLog 259 RMD160 5903f3705671cc0c8ff1a9d1525fb08fee1c72c5 SHA1 8d062d594f2336ad2c943bc6f25d4ecbd65d9a11 SHA256 1d2a3f88e35d900d646bdae02430eaf160661ee08109b93748f67463a3d1f87b
+MD5 f6b2eb4f4b549f362da76f3fb0b37f25 ChangeLog 259
+RMD160 5903f3705671cc0c8ff1a9d1525fb08fee1c72c5 ChangeLog 259
+SHA256 1d2a3f88e35d900d646bdae02430eaf160661ee08109b93748f67463a3d1f87b ChangeLog 259
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
+MD5 1e678929a9fec6632e227bdf2262e9a1 metadata.xml 170
+RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 metadata.xml 170
+SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 metadata.xml 170
+MD5 6031057f170ba3e39d873476919294cf files/digest-glimmerhmm-3.0.1 256
+RMD160 30de1bc3c8be7819528bdbaea8be47a38d92b3a5 files/digest-glimmerhmm-3.0.1 256
+SHA256 a5ceb414b56313f97ef383cc3debda25408bcf877376fc456319a55e6f4f769e files/digest-glimmerhmm-3.0.1 256
diff --git a/sci-biology/glimmerhmm/files/digest-glimmerhmm-3.0.1 b/sci-biology/glimmerhmm/files/digest-glimmerhmm-3.0.1
new file mode 100644
index 000000000..9ab418485
--- /dev/null
+++ b/sci-biology/glimmerhmm/files/digest-glimmerhmm-3.0.1
@@ -0,0 +1,3 @@
+MD5 e98e0bad04507b7f661e6b9876c3d1f6 GlimmerHMM-3.0.1.tar.gz 45475952
+RMD160 273cb74458e3f444cd9f8ca9f6618335aea5465f GlimmerHMM-3.0.1.tar.gz 45475952
+SHA256 c956838a398483003ff1af867c65aca082b82340d8b302b9ada77d1b246954e4 GlimmerHMM-3.0.1.tar.gz 45475952
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 000000000..5a81f47b0
--- /dev/null
+++ b/sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+MY_P=GlimmerHMM
+
+DESCRIPTION="A 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 000000000..7e3286984
--- /dev/null
+++ b/sci-biology/glimmerhmm/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>