sci-biology/glimmer: new package sci-biology/glimmer (bug 170895)

svn path=/sunrise/; revision=3226

5 files changed, 71 insertions, 0 deletions

diff --git a/sci-biology/glimmer/ChangeLog b/sci-biology/glimmer/ChangeLog
new file mode 100644
index 000000000..8a3159a2d
--- /dev/null
+++ b/sci-biology/glimmer/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-biology/glimmer
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  14 Mar 2007; AK <gentoo@horizon.ath.cx> +glimmer-3.02.ebuild,
+  +metadata.xml:
+  new package sci-biology/glimmer (bug 170895)
+
diff --git a/sci-biology/glimmer/Manifest b/sci-biology/glimmer/Manifest
new file mode 100644
index 000000000..502c48520
--- /dev/null
+++ b/sci-biology/glimmer/Manifest
@@ -0,0 +1,16 @@
+DIST glimmer302.tar.gz 5637075 RMD160 bc29bb045f7a4179504cb3843741393f42e11ab8 SHA1 e2f27fdab82cd8978f1452bfcd4c0287c52b77b7 SHA256 a1e422ee56f495f9f99e1741ba2043f026fc8182afcc47cb20cfd2d989537221
+EBUILD glimmer-3.02.ebuild 964 RMD160 3a4051ee0415b58b062e337b7a143875fb6eb358 SHA1 2e4d23e360e62ce31d1bc81a6d9b0a2b0535a946 SHA256 2c7a8fe4104b1fdae2a1bcb37d66b7125f9e9a205be26ee40fed168ea89920a3
+MD5 a862b4f25a640374584f56b64c08b737 glimmer-3.02.ebuild 964
+RMD160 3a4051ee0415b58b062e337b7a143875fb6eb358 glimmer-3.02.ebuild 964
+SHA256 2c7a8fe4104b1fdae2a1bcb37d66b7125f9e9a205be26ee40fed168ea89920a3 glimmer-3.02.ebuild 964
+MISC ChangeLog 249 RMD160 b07216270319744dacff5e703451e3f0cd91a018 SHA1 6d8b4f8093708bb34f961bb72a8d00a54f78f283 SHA256 61b355b473481952eb0826fd22dc5edb5cafc7e4696ddcd83dd2d1e34e695214
+MD5 b1b54dd03641d1cf13a30ed56523d41a ChangeLog 249
+RMD160 b07216270319744dacff5e703451e3f0cd91a018 ChangeLog 249
+SHA256 61b355b473481952eb0826fd22dc5edb5cafc7e4696ddcd83dd2d1e34e695214 ChangeLog 249
+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 0598b7144226d863734ebb1b24afbf42 files/digest-glimmer-3.02 235
+RMD160 9847204829229587d689348ec41f339162f447c6 files/digest-glimmer-3.02 235
+SHA256 8f9193b635bdf44fde42e859c109f9b3d0edf3b5e1eba9ddea979671561ffedd files/digest-glimmer-3.02 235
diff --git a/sci-biology/glimmer/files/digest-glimmer-3.02 b/sci-biology/glimmer/files/digest-glimmer-3.02
new file mode 100644
index 000000000..b724ad949
--- /dev/null
+++ b/sci-biology/glimmer/files/digest-glimmer-3.02
@@ -0,0 +1,3 @@
+MD5 3e933b79c7d019eb48fa87b9fda1e1ee glimmer302.tar.gz 5637075
+RMD160 bc29bb045f7a4179504cb3843741393f42e11ab8 glimmer302.tar.gz 5637075
+SHA256 a1e422ee56f495f9f99e1741ba2043f026fc8182afcc47cb20cfd2d989537221 glimmer302.tar.gz 5637075
diff --git a/sci-biology/glimmer/glimmer-3.02.ebuild b/sci-biology/glimmer/glimmer-3.02.ebuild
new file mode 100644
index 000000000..1b0cae43b
--- /dev/null
+++ b/sci-biology/glimmer/glimmer-3.02.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit versionator
+
+MY_P=glimmer${PV}
+MY_PV=$(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/glimmer/glimmer${MY_PV}.tar.gz"
+
+LICENSE="glimmer"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S=${WORKDIR}/${MY_P}
+
+src_compile() {
+	sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts' \
+		-e 's|\(set glimmerpath =\).*|\1 /usr/bin' scripts/*
+	cd src
+	emake || die "emake failed"
+}
+
+src_install() {
+	dobin bin/{anomaly,build-icm,entropy-score,glimmer3,multi-extract,start-codon-distrib,uncovered,build-fixed,entropy-profile,extract,long-orfs,score-fixed,window-acgt}
+
+	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 000000000..7e3286984
--- /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>