Version bump

4 files changed, 85 insertions, 0 deletions

diff --git a/sci-biology/wgs-assembler/ChangeLog b/sci-biology/wgs-assembler/ChangeLog
new file mode 100644
index 000000000..e003d5338
--- /dev/null
+++ b/sci-biology/wgs-assembler/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-biology/wgs-assembler
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/wgs-assembler/ChangeLog,v 1.1 2009/06/05 15:16:05 weaver Exp $
+
+  02 Aug 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
+  Version bump
+
+*wgs-assembler-5.3 (05 Jun 2009)
+
+  05 Jun 2009; Andrey Kislyuk <weaver@gentoo.org> +wgs-assembler-5.3.ebuild:
+  New package, ebuild written by me
+
diff --git a/sci-biology/wgs-assembler/Manifest b/sci-biology/wgs-assembler/Manifest
new file mode 100644
index 000000000..d7c2cc565
--- /dev/null
+++ b/sci-biology/wgs-assembler/Manifest
@@ -0,0 +1,6 @@
+DIST wgs-5.3.tar.bz2 1755488 RMD160 fcfb19a2063f936ad197130b14370c69add08b78 SHA1 5430df65c1f0c5057607a0e4c58113a1495438c3 SHA256 929b7429e279018a1f6a1a82206a925d8e7bd024b21f57660e51e1766553db43
+DIST wgs-5.4.tar.bz2 1876180 RMD160 1f8a82f7523509ef271c7e99d560f68367ab16a1 SHA1 2dbc316c8307181246a22d622c824885be373333 SHA256 698b22bd63fa2bb4fe7f164a92c92f82474bc8fc64c37704258ebb3bdc86d7bf
+EBUILD wgs-assembler-5.3.ebuild 1257 RMD160 3eaf1e5dff7dd671acdc15c6f56c5a6395f304ca SHA1 2ca50b96e5a24d3c8146451730099291563fb7da SHA256 54bd2506b49d7b49950dce0079a9141cca64c11e66aa392787640ed171548947
+EBUILD wgs-assembler-5.4.ebuild 1512 RMD160 92ef12d18960de6ed55f63394eb9ed8b4e1e0ac2 SHA1 bd4f0c1f78def100d7085a225da6e648f7c4300f SHA256 a484371627c3062c7b24280e67cd8ebeacc039b17144e8957487726f760329d1
+MISC ChangeLog 371 RMD160 03736c2ef687f07a275f68345acf0f9dbd3bae1c SHA1 30a3746fbf9c5b8cc0408243e43229a8473eeb9a SHA256 409667672e196fae4b9a6e5ddd2ab6c2a6f2eed1ef4aad62b6c350d12f3f1618
+MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/wgs-assembler/metadata.xml b/sci-biology/wgs-assembler/metadata.xml
new file mode 100644
index 000000000..3302123e5
--- /dev/null
+++ b/sci-biology/wgs-assembler/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/wgs-assembler/wgs-assembler-5.4.ebuild b/sci-biology/wgs-assembler/wgs-assembler-5.4.ebuild
new file mode 100644
index 000000000..165f2b068
--- /dev/null
+++ b/sci-biology/wgs-assembler/wgs-assembler-5.4.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/wgs-assembler/wgs-assembler-5.3.ebuild,v 1.1 2009/06/05 15:16:05 weaver Exp $
+
+EAPI="2"
+
+inherit eutils
+
+DESCRIPTION="Whole-genome shotgun assembler based on the Celera Assembler"
+HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"
+SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86 ~amd64"
+
+DEPEND="x11-libs/libXt"
+RDEPEND="${DEPEND}
+	app-shells/tcsh
+	dev-perl/Log-Log4perl"
+
+S="${WORKDIR}/wgs-${PV}"
+
+src_configure() {
+	cd "${S}/kmer"
+	./configure.sh || die
+}
+
+src_compile() {
+	# not really an install target
+	# WARNING: untracked failure compiling the second target
+	emake -C kmer -j1 install || die
+	emake -C src -j1 SITE_NAME=LOCAL || die
+}
+
+src_install() {
+	OSTYPE=$(uname)
+	MACHTYPE=$(uname -m)
+	MACHTYPE=${MACHTYPE/x86_64/amd64}
+	MY_S="${OSTYPE}-${MACHTYPE}"
+	sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die
+
+	sed -i '/sub getBinDirectory/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die
+	sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die
+
+	dobin kmer/${MY_S}/bin/* || die
+	dolib.a kmer/${MY_S}/lib/* || die
+
+	insinto /usr/share/${PN}
+	doins -r ${MY_S}/bin/spec
+	insinto /usr/share/${PN}/lib
+	doins -r ${MY_S}/bin/TIGR || die
+	rm -rf ${MY_S}/bin/{TIGR,spec}
+	dobin ${MY_S}/bin/* || die
+	dolib.a ${MY_S}/lib/* || die
+	dodoc README
+}