Version bump

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

4 files changed, 79 insertions, 60 deletions

diff --git a/sci-biology/wgs-assembler/ChangeLog b/sci-biology/wgs-assembler/ChangeLog
index d025702a3335..aa6b729201d7 100644
--- a/sci-biology/wgs-assembler/ChangeLog
+++ b/sci-biology/wgs-assembler/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/wgs-assembler
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/wgs-assembler/ChangeLog,v 1.5 2010/03/29 09:42:24 pacho Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/wgs-assembler/ChangeLog,v 1.6 2010/05/07 20:00:24 weaver Exp $
+
+*wgs-assembler-6.1 (07 May 2010)
+
+  07 May 2010; Andrey Kislyuk <weaver@gentoo.org> -wgs-assembler-5.3.ebuild,
+  +wgs-assembler-6.1.ebuild:
+  Version bump
 
   29 Mar 2010; Pacho Ramos <pacho@gentoo.org> wgs-assembler-5.4.ebuild:
   amd64 stable, bug 298775
diff --git a/sci-biology/wgs-assembler/Manifest b/sci-biology/wgs-assembler/Manifest
index 48f8457ec623..aa231e504b46 100644
--- a/sci-biology/wgs-assembler/Manifest
+++ b/sci-biology/wgs-assembler/Manifest
@@ -1,16 +1,6 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
-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
+DIST wgs-6.1.tar.bz2 1900084 RMD160 2b5b6df38d02da83cad630059cbbe798ea669a58 SHA1 d29401223a0b2e1a65b6f9db40441ad41e2d10ec SHA256 e00c1b64e857ea01f7e9a9f115dd91e290a380ccda217dd6a386f57754a3cff8
 EBUILD wgs-assembler-5.4.ebuild 1986 RMD160 67db26654b69651ebb0c67a564b71805f51821b6 SHA1 c71ce6a1c704fb836bb5cb46a8c0c3bfcd0125a8 SHA256 6125ec4b48604ce4535bdae04eabad1b2710e679004d202847325fe2726f06e1
-MISC ChangeLog 806 RMD160 1306c706108c8eb66efd22888049fac0b44025c5 SHA1 798e4d397994d50e267e3cf695dffdcada402d20 SHA256 c6d0c4f1c1bd0289ee1579f896244e350ceb02e383c1fb0213ad62b04299e414
+EBUILD wgs-assembler-6.1.ebuild 1989 RMD160 491259f5598dcef0bfe2ebf96a7a86e35b1bf2f6 SHA1 550661c5957500ab4c8bab0b17d5161ae7c12bf7 SHA256 116d85f93fd578e071850103ee08f1189f93a160af3a79fd086a568335b8fd88
+MISC ChangeLog 963 RMD160 e5f6962b818b0fe994068674785beec5000e6f93 SHA1 be73d04714d9e7ebd50371915e8ec00382505406 SHA256 ebd5bf0c4f8b01f5bfd7d75f5f664ddc6c094e82782329e9e10bcfc8abd34552
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.14 (GNU/Linux)
-
-iEYEARECAAYFAkuwdgUACgkQCaWpQKGI+9T+MACfdcqNylKBUx+pK7uZEmfHUmVB
-EhoAn3KOMh5rkOaE81vNB4zaJBZY5Bom
-=L/YG
------END PGP SIGNATURE-----
diff --git a/sci-biology/wgs-assembler/wgs-assembler-5.3.ebuild b/sci-biology/wgs-assembler/wgs-assembler-5.3.ebuild
deleted file mode 100644
index 4b95c05a3b7c..000000000000
--- a/sci-biology/wgs-assembler/wgs-assembler-5.3.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# 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-${PV}"
-
-src_compile() {
-	emake -C src -j1 SITE_NAME=LOCAL || die
-}
-
-src_install() {
-	OSTYPE=$(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 $MY_S -name '*.p*') || die
-	insinto /usr/share/${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
-}
diff --git a/sci-biology/wgs-assembler/wgs-assembler-6.1.ebuild b/sci-biology/wgs-assembler/wgs-assembler-6.1.ebuild
new file mode 100644
index 000000000000..d6b250aa990e
--- /dev/null
+++ b/sci-biology/wgs-assembler/wgs-assembler-6.1.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/wgs-assembler/wgs-assembler-6.1.ebuild,v 1.1 2010/05/07 20:00:24 weaver Exp $
+
+EAPI="2"
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG"
+HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"
+SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="x11-libs/libXt"
+RDEPEND="${DEPEND}
+	app-shells/tcsh
+	dev-perl/Log-Log4perl"
+
+S="${WORKDIR}/wgs-${PV}"
+
+src_configure() {
+	sed -i -e "s/CC *= *gcc/CC = $(tc-getCC)/" \
+		-e "s/CXX *= *g++/CXX = $(tc-getCXX)/" \
+		"${S}"/src/c_make.as || die
+	sed -i -e "s/CC *:=.*/CC := $(tc-getCC)/" \
+		-e "s/CXX *:=.*/CXX := $(tc-getCXX)/" \
+		"${S}"/kmer/configure.sh || die
+	cd "${S}/kmer"
+	./configure.sh || die
+}
+
+src_compile() {
+	# not really an install target
+	emake -C kmer -j1 install || die
+	emake -C src -j1 SITE_NAME=LOCAL || die
+}
+
+src_install() {
+	OSTYPE=$(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 '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die
+	sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die
+
+	dobin kmer/${MY_S}/bin/* || die
+	insinto /usr/$(get_libdir)/${PN}
+	doins kmer/${MY_S}/lib/* || die
+	# Collisions
+	# dolib.a kmer/${MY_S}/lib/* || die
+	insinto /usr/include/${PN}
+	doins kmer/${MY_S}/include/*
+
+	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
+}