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* [gentoo-commits] proj/sci:master commit in: sci-biology/wgs-assembler/
@ 2012-01-27 20:22 Martin Mokrejs
  0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2012-01-27 20:22 UTC (permalink / raw
  To: gentoo-commits

commit:     965af5d33a809748be2547a9287fd90d121fa512
Author:     Martin Mokrejs <mmokrejs <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 27 21:24:06 2012 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 27 21:24:06 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=965af5d3

sci-biology/wgs-assembler-7.0: version bump, would be nice if we could stop compilation of the kmer/ subdir (an r1916 snapshot) and DEPEND on the external http://kmer.sourceforge.net complete bundle instead

(Portage version: 2.1.10.44/git/Linux i686, unsigned Manifest commit)

---
 sci-biology/wgs-assembler/ChangeLog                |   12 ++++
 sci-biology/wgs-assembler/metadata.xml             |    9 +++
 sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild |   70 ++++++++++++++++++++
 3 files changed, 91 insertions(+), 0 deletions(-)

diff --git a/sci-biology/wgs-assembler/ChangeLog b/sci-biology/wgs-assembler/ChangeLog
new file mode 100644
index 0000000..24fb71d
--- /dev/null
+++ b/sci-biology/wgs-assembler/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-biology/wgs-assembler
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*wgs-assembler-7.0 (27 Jan 2012)
+
+  27 Jan 2012; mmokrejs@fold.natur.cuni.cz +metadata.xml,
+  +wgs-assembler-7.0.ebuild:
+  sci-biology/wgs-assembler-7.0: version bump, would be nice if we could stop
+  compilation of the kmer/ subdir (an r1916 snapshot) and DEPEND on the external
+  http://kmer.sourceforge.net complete bundle instead
+

diff --git a/sci-biology/wgs-assembler/metadata.xml b/sci-biology/wgs-assembler/metadata.xml
new file mode 100644
index 0000000..3302123
--- /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-7.0.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild
new file mode 100644
index 0000000..b75a5b7
--- /dev/null
+++ b/sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2012 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 1.3 2011/03/20 20:19:27 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
+	!x11-terms/terminator"
+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
+}



^ permalink raw reply related	[flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/wgs-assembler/
@ 2013-02-18 12:11 Justin Lecher
  0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2013-02-18 12:11 UTC (permalink / raw
  To: gentoo-commits

commit:     091646173edca5b62fc12d430879378d868ae45a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 18 12:11:06 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Feb 18 12:11:06 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=09164617

newer version in the tree

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 sci-biology/wgs-assembler/ChangeLog                |   12 ----
 sci-biology/wgs-assembler/metadata.xml             |    9 ---
 sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild |   70 --------------------
 3 files changed, 0 insertions(+), 91 deletions(-)

diff --git a/sci-biology/wgs-assembler/ChangeLog b/sci-biology/wgs-assembler/ChangeLog
deleted file mode 100644
index 24fb71d..0000000
--- a/sci-biology/wgs-assembler/ChangeLog
+++ /dev/null
@@ -1,12 +0,0 @@
-# ChangeLog for sci-biology/wgs-assembler
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*wgs-assembler-7.0 (27 Jan 2012)
-
-  27 Jan 2012; mmokrejs@fold.natur.cuni.cz +metadata.xml,
-  +wgs-assembler-7.0.ebuild:
-  sci-biology/wgs-assembler-7.0: version bump, would be nice if we could stop
-  compilation of the kmer/ subdir (an r1916 snapshot) and DEPEND on the external
-  http://kmer.sourceforge.net complete bundle instead
-

diff --git a/sci-biology/wgs-assembler/metadata.xml b/sci-biology/wgs-assembler/metadata.xml
deleted file mode 100644
index 3302123..0000000
--- a/sci-biology/wgs-assembler/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?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-7.0.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild
deleted file mode 100644
index b75a5b7..0000000
--- a/sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2012 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 1.3 2011/03/20 20:19:27 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
-	!x11-terms/terminator"
-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
-}


^ permalink raw reply related	[flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/wgs-assembler/
@ 2015-04-18  1:11 Martin Mokrejs
  0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-04-18  1:11 UTC (permalink / raw
  To: gentoo-commits

commit:     851ba2104e66025e2a60f260d2851d57dba3ef44
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 18 01:10:48 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 18 01:10:48 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=851ba210

sci-biology/wgs-assembler: version bumps; did not check if the LDFLAGS part of the v7.0 patch should be carried over; CFLAGS seems are already handled properly by current code; 8.3rc1 dies at: install: cannot stat 'Linux-amd64/bin/TIGR': No such file or directory

Package-Manager: portage-2.2.18

 sci-biology/wgs-assembler/ChangeLog                | 13 ++++
 sci-biology/wgs-assembler/metadata.xml             |  5 ++
 sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild | 78 +++++++++++++++++++++
 .../wgs-assembler/wgs-assembler-8.3_rc1.ebuild     | 81 ++++++++++++++++++++++
 4 files changed, 177 insertions(+)

diff --git a/sci-biology/wgs-assembler/ChangeLog b/sci-biology/wgs-assembler/ChangeLog
new file mode 100644
index 0000000..6299944
--- /dev/null
+++ b/sci-biology/wgs-assembler/ChangeLog
@@ -0,0 +1,13 @@
+# ChangeLog for sci-biology/wgs-assembler
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*wgs-assembler-8.2 (18 Apr 2015)
+*wgs-assembler-8.3_rc1 (18 Apr 2015)
+
+  18 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
+  +wgs-assembler-8.2.ebuild, +wgs-assembler-8.3_rc1.ebuild:
+  sci-biology/wgs-assembler: version bumps; did not check if the LDFLAGS part of
+  the v7.0 patch should be carried over; CFLAGS seems are already handled
+  properly by current code; 8.3rc1 dies at: install: cannot stat 'Linux-
+  amd64/bin/TIGR': No such file or directory

diff --git a/sci-biology/wgs-assembler/metadata.xml b/sci-biology/wgs-assembler/metadata.xml
new file mode 100644
index 0000000..f17a827
--- /dev/null
+++ b/sci-biology/wgs-assembler/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>sci-biology</herd>
+</pkgmetadata>

diff --git a/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild
new file mode 100644
index 0000000..831af99
--- /dev/null
+++ b/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild,v 1.3 2012/11/13 19:19:00 nativemad Exp $
+
+EAPI=4
+
+PYTHON_DEPEND=2
+
+inherit eutils python toolchain-funcs
+
+DESCRIPTION="De novo whole-genome shotgun DNA sequence assembler also known as 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"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND="
+	x11-libs/libXt
+	!x11-terms/terminator"
+RDEPEND="${DEPEND}
+	app-shells/tcsh
+	dev-perl/Log-Log4perl"
+
+S="${WORKDIR}/wgs-${PV}"
+
+pkg_setup() {
+	python_set_active_version 2
+	python_pkg_setup
+}
+
+src_prepare() {
+	# epatch \
+	# 	"${FILESDIR}"/${P}-build.patch
+	tc-export CC CXX
+}
+
+src_configure() {
+	cd "${S}/kmer"
+	./configure.sh || die
+}
+
+src_compile() {
+	# not really an install target
+	emake -C kmer -j1 install
+	emake -C src -j1 SITE_NAME=LOCAL
+}
+
+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/*
+	insinto /usr/$(get_libdir)/${PN}
+	use static-libs && doins kmer/${MY_S}/lib/*
+
+	insinto /usr/include/${PN}
+	doins kmer/${MY_S}/include/*
+
+	insinto /usr/share/${PN}/lib
+	doins -r ${MY_S}/bin/TIGR
+	rm -rf ${MY_S}/bin/TIGR || die
+	dobin ${MY_S}/bin/*
+	use static-libs && dolib.a ${MY_S}/lib/*
+	dodoc README
+
+	# avoid file collision
+	rm -f ${D}/usr/bin/jellyfish
+}

diff --git a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc1.ebuild b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc1.ebuild
new file mode 100644
index 0000000..73518ed
--- /dev/null
+++ b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc1.ebuild
@@ -0,0 +1,81 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild,v 1.3 2012/11/13 19:19:00 nativemad Exp $
+
+EAPI=4
+
+PYTHON_DEPEND=2
+
+inherit eutils python toolchain-funcs
+
+MY_PV="8.3rc1"
+
+DESCRIPTION="De novo whole-genome shotgun DNA sequence assembler also known as Celera Assembler and CABOG"
+HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"
+#SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2"
+SRC_URI="http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-8.3/wgs-8.3rc1.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND="
+	x11-libs/libXt
+	!x11-terms/terminator"
+RDEPEND="${DEPEND}
+	app-shells/tcsh
+	dev-perl/Log-Log4perl"
+
+S="${WORKDIR}/wgs-${MY_PV}"
+
+pkg_setup() {
+	python_set_active_version 2
+	python_pkg_setup
+}
+
+src_prepare() {
+	# epatch \
+	# 	"${FILESDIR}"/${P}-build.patch
+	tc-export CC CXX
+}
+
+src_configure() {
+	cd "${S}/kmer"
+	./configure.sh || die
+}
+
+src_compile() {
+	# not really an install target
+	emake -C kmer -j1 install
+	emake -C src -j1 SITE_NAME=LOCAL
+}
+
+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/*
+	insinto /usr/$(get_libdir)/${PN}
+	use static-libs && doins kmer/${MY_S}/lib/*
+
+	insinto /usr/include/${PN}
+	doins kmer/${MY_S}/include/*
+
+	insinto /usr/share/${PN}/lib
+	doins -r ${MY_S}/bin/TIGR
+	rm -rf ${MY_S}/bin/TIGR || die
+	dobin ${MY_S}/bin/*
+	use static-libs && dolib.a ${MY_S}/lib/*
+	dodoc README
+
+	# avoid file collision
+	rm -f ${D}/usr/bin/jellyfish
+}


^ permalink raw reply related	[flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/wgs-assembler/
@ 2015-05-25 23:30 Martin Mokrejs
  0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-05-25 23:30 UTC (permalink / raw
  To: gentoo-commits

commit:     79bbc72e8f4f267272b3b7310165bd582ce50a46
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 25 23:29:14 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 25 23:29:14 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=79bbc72e

version bump; quote variables

Package-Manager: portage-2.2.18

 sci-biology/wgs-assembler/ChangeLog                |  6 ++++++
 sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild | 24 ++++++++++-----------
 ...8.3_rc1.ebuild => wgs-assembler-8.3_rc2.ebuild} | 25 +++++++++++-----------
 3 files changed, 30 insertions(+), 25 deletions(-)

diff --git a/sci-biology/wgs-assembler/ChangeLog b/sci-biology/wgs-assembler/ChangeLog
index 6299944..d52282e 100644
--- a/sci-biology/wgs-assembler/ChangeLog
+++ b/sci-biology/wgs-assembler/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*wgs-assembler-8.3_rc2 (25 May 2015)
+
+  25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +wgs-assembler-8.3_rc2.ebuild, -wgs-assembler-8.3_rc1.ebuild:
+  version bump
+
 *wgs-assembler-8.2 (18 Apr 2015)
 *wgs-assembler-8.3_rc1 (18 Apr 2015)
 

diff --git a/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild
index 831af99..c9e5641 100644
--- a/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild
+++ b/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild,v 1.3 2012/11/13 19:19:00 nativemad Exp $
 
-EAPI=4
+EAPI=5
 
 PYTHON_DEPEND=2
 
@@ -59,20 +59,20 @@ src_install() {
 	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/${MY_S}/bin/*
-	insinto /usr/$(get_libdir)/${PN}
-	use static-libs && doins kmer/${MY_S}/lib/*
+	dobin kmer/"${MY_S}"/bin/*
+	insinto /usr/"$(get_libdir)/${PN}"
+	use static-libs && doins kmer/"${MY_S}"/lib/*
 
-	insinto /usr/include/${PN}
-	doins kmer/${MY_S}/include/*
+	insinto /usr/include/"${PN}"
+	doins kmer/"${MY_S}"/include/*
 
-	insinto /usr/share/${PN}/lib
-	doins -r ${MY_S}/bin/TIGR
-	rm -rf ${MY_S}/bin/TIGR || die
-	dobin ${MY_S}/bin/*
-	use static-libs && dolib.a ${MY_S}/lib/*
+	insinto /usr/share/"${PN}"/lib
+	doins -r "${MY_S}"/bin/TIGR
+	rm -rf "${MY_S}"/bin/TIGR || die
+	dobin "${MY_S}"/bin/*
+	use static-libs && dolib.a "${MY_S}"/lib/*
 	dodoc README
 
 	# avoid file collision
-	rm -f ${D}/usr/bin/jellyfish
+	rm -f "${D}"/usr/bin/jellyfish
 }

diff --git a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc1.ebuild b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
similarity index 80%
rename from sci-biology/wgs-assembler/wgs-assembler-8.3_rc1.ebuild
rename to sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
index 73518ed..22a765b 100644
--- a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc1.ebuild
+++ b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
@@ -2,18 +2,17 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild,v 1.3 2012/11/13 19:19:00 nativemad Exp $
 
-EAPI=4
+EAPI=5
 
 PYTHON_DEPEND=2
 
 inherit eutils python toolchain-funcs
 
-MY_PV="8.3rc1"
+MY_PV="${PV/_}" # convert from _rc2 to rc2
 
 DESCRIPTION="De novo whole-genome shotgun DNA sequence assembler also known as Celera Assembler and CABOG"
 HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"
-#SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2"
-SRC_URI="http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-8.3/wgs-8.3rc1.tar.bz2"
+SRC_URI="http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-8.3/wgs-${MY_PV}.tar.bz2"
 
 LICENSE="GPL-2"
 SLOT="0"
@@ -62,20 +61,20 @@ src_install() {
 	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/${MY_S}/bin/*
-	insinto /usr/$(get_libdir)/${PN}
-	use static-libs && doins kmer/${MY_S}/lib/*
+	dobin kmer/"${MY_S}"/bin/*
+	insinto /usr/$(get_libdir)/"${PN}"
+	use static-libs && doins kmer/"${MY_S}"/lib/*
 
-	insinto /usr/include/${PN}
-	doins kmer/${MY_S}/include/*
+	insinto /usr/include/"${PN}"
+	doins kmer/"${MY_S}"/include/*
 
 	insinto /usr/share/${PN}/lib
-	doins -r ${MY_S}/bin/TIGR
-	rm -rf ${MY_S}/bin/TIGR || die
-	dobin ${MY_S}/bin/*
+	doins -r "${MY_S}"/bin/TIGR
+	rm -rf "${MY_S}"/bin/TIGR || die
+	dobin "${MY_S}"/bin/*
 	use static-libs && dolib.a ${MY_S}/lib/*
 	dodoc README
 
 	# avoid file collision
-	rm -f ${D}/usr/bin/jellyfish
+	rm -f "${D}"/usr/bin/jellyfish
 }


^ permalink raw reply related	[flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/wgs-assembler/
@ 2015-09-21 19:44 Justin Lecher
  0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2015-09-21 19:44 UTC (permalink / raw
  To: gentoo-commits

commit:     215a7570a21fb795331b069f13560156fbad4e76
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 21 19:31:30 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 21 19:31:30 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=215a7570

sci-biology/wgs-assembler: Use new python eclass

Package-Manager: portage-2.2.20.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild | 78 ----------------------
 .../wgs-assembler/wgs-assembler-8.3_rc2.ebuild     | 17 ++---
 2 files changed, 6 insertions(+), 89 deletions(-)

diff --git a/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild
deleted file mode 100644
index 5f4b775..0000000
--- a/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild
+++ /dev/null
@@ -1,78 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_DEPEND=2
-
-inherit eutils python toolchain-funcs
-
-DESCRIPTION="De novo whole-genome shotgun DNA sequence assembler also known as 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"
-KEYWORDS="~amd64 ~x86"
-IUSE="static-libs"
-
-DEPEND="
-	x11-libs/libXt
-	!x11-terms/terminator"
-RDEPEND="${DEPEND}
-	app-shells/tcsh
-	dev-perl/Log-Log4perl"
-
-S="${WORKDIR}/wgs-${PV}"
-
-pkg_setup() {
-	python_set_active_version 2
-	python_pkg_setup
-}
-
-src_prepare() {
-	# epatch \
-	# 	"${FILESDIR}"/${P}-build.patch
-	tc-export CC CXX
-}
-
-src_configure() {
-	cd "${S}/kmer"
-	./configure.sh || die
-}
-
-src_compile() {
-	# not really an install target
-	emake -C kmer -j1 install
-	emake -C src -j1 SITE_NAME=LOCAL
-}
-
-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/*
-	insinto /usr/"$(get_libdir)/${PN}"
-	use static-libs && doins kmer/"${MY_S}"/lib/*
-
-	insinto /usr/include/"${PN}"
-	doins kmer/"${MY_S}"/include/*
-
-	insinto /usr/share/"${PN}"/lib
-	doins -r "${MY_S}"/bin/TIGR
-	rm -rf "${MY_S}"/bin/TIGR || die
-	dobin "${MY_S}"/bin/*
-	use static-libs && dolib.a "${MY_S}"/lib/*
-	dodoc README
-
-	# avoid file collision
-	rm -f "${D}"/usr/bin/jellyfish
-}

diff --git a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
index 9b481a2..e1b5585 100644
--- a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
+++ b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
@@ -4,15 +4,15 @@
 
 EAPI=5
 
-PYTHON_DEPEND=2
+PYTHON_COMPAT=( python2_7 )
 
-inherit eutils python toolchain-funcs
+inherit eutils python-single-r1 toolchain-funcs
 
 MY_PV="${PV/_}" # convert from _rc2 to rc2
 
-DESCRIPTION="De novo whole-genome shotgun DNA sequence assembler also known as Celera Assembler and CABOG"
+DESCRIPTION="De novo whole-genome shotgun DNA sequence assembler (Celera Assembler and CABOG)"
 HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"
-SRC_URI="http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-8.3/wgs-${MY_PV}.tar.bz2"
+SRC_URI="http://sourceforge.net/projects/${PN}/files/${PN}/wgs-8.3/wgs-${MY_PV}.tar.bz2"
 
 LICENSE="GPL-2"
 SLOT="0"
@@ -28,11 +28,6 @@ RDEPEND="${DEPEND}
 
 S="${WORKDIR}/wgs-${MY_PV}"
 
-pkg_setup() {
-	python_set_active_version 2
-	python_pkg_setup
-}
-
 src_prepare() {
 	# epatch \
 	# 	"${FILESDIR}"/${P}-build.patch
@@ -40,7 +35,7 @@ src_prepare() {
 }
 
 src_configure() {
-	cd "${S}/kmer"
+	cd "${S}/kmer" || die
 	./configure.sh || die
 }
 
@@ -76,5 +71,5 @@ src_install() {
 	dodoc README
 
 	# avoid file collision
-	rm -f "${D}"/usr/bin/jellyfish
+	rm -f "${D}"/usr/bin/jellyfish || die
 }


^ permalink raw reply related	[flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/wgs-assembler/
@ 2016-04-08 18:25 Martin Mokrejs
  0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2016-04-08 18:25 UTC (permalink / raw
  To: gentoo-commits

commit:     ca3b609296cd640836ab9838ec1a838b53b78dcd
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr  8 18:21:34 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr  8 18:21:34 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ca3b6092

sci-biology/wgs-assembler: improve package description

Package-Manager: portage-2.2.28

 sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
index e1b5585..35f7f58 100644
--- a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
+++ b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -10,7 +10,7 @@ inherit eutils python-single-r1 toolchain-funcs
 
 MY_PV="${PV/_}" # convert from _rc2 to rc2
 
-DESCRIPTION="De novo whole-genome shotgun DNA sequence assembler (Celera Assembler and CABOG)"
+DESCRIPTION="De novo whole-genome shotgun DNA sequence OLC assembler (Celera Assembler, CABOG)"
 HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"
 SRC_URI="http://sourceforge.net/projects/${PN}/files/${PN}/wgs-8.3/wgs-${MY_PV}.tar.bz2"
 


^ permalink raw reply related	[flat|nested] 6+ messages in thread
end of thread, other threads:[~2016-04-08 18:25 UTC | newest]

Thread overview: 6+ messages (download: mbox.gz follow: Atom feed
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2016-04-08 18:25 Martin Mokrejs
2015-05-25 23:30 Martin Mokrejs
2015-04-18  1:11 Martin Mokrejs
2013-02-18 12:11 Justin Lecher
2012-01-27 20:22 Martin Mokrejs

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