* [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
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2012-01-27 20:22 Martin Mokrejs
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