* [gentoo-commits] gentoo-x86 commit in sci-biology/allpaths: ChangeLog allpaths-3.1.ebuild
@ 2010-01-26 20:43 Andrey Kislyuk (weaver)
0 siblings, 0 replies; 3+ messages in thread
From: Andrey Kislyuk (weaver) @ 2010-01-26 20:43 UTC (permalink / raw
To: gentoo-commits
weaver 10/01/26 20:43:21
Modified: ChangeLog
Added: allpaths-3.1.ebuild
Log:
Version bump
(Portage version: 2.2_rc30/cvs/Linux x86_64, RepoMan options: --force)
Revision Changes Path
1.6 sci-biology/allpaths/ChangeLog
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/allpaths/ChangeLog?rev=1.6&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/allpaths/ChangeLog?rev=1.6&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/allpaths/ChangeLog?r1=1.5&r2=1.6
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/allpaths/ChangeLog,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- ChangeLog 3 Jan 2010 14:08:56 -0000 1.5
+++ ChangeLog 26 Jan 2010 20:43:21 -0000 1.6
@@ -1,6 +1,11 @@
# ChangeLog for sci-biology/allpaths
# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/ChangeLog,v 1.5 2010/01/03 14:08:56 pacho Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/ChangeLog,v 1.6 2010/01/26 20:43:21 weaver Exp $
+
+*allpaths-3.1 (26 Jan 2010)
+
+ 26 Jan 2010; Andrey Kislyuk <weaver@gentoo.org> +allpaths-3.1.ebuild:
+ Version bump
03 Jan 2010; Pacho Ramos <pacho@gentoo.org> allpaths-2.0.ebuild:
amd64 stable, bug 290927
1.1 sci-biology/allpaths/allpaths-3.1.ebuild
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/allpaths/allpaths-3.1.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/allpaths/allpaths-3.1.ebuild?rev=1.1&content-type=text/plain
Index: allpaths-3.1.ebuild
===================================================================
# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/allpaths-3.1.ebuild,v 1.1 2010/01/26 20:43:21 weaver Exp $
EAPI="2"
inherit base
DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
SRC_URI="ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/allpaths-${PV}.tgz
ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/AllPathsV3_Manual_r1.0.docx"
LICENSE="Whitehead-MIT"
SLOT="3"
IUSE=""
KEYWORDS="~amd64"
DEPEND=">=sys-devel/gcc-4.3.2"
RDEPEND=""
S="${WORKDIR}/AllPaths"
src_compile() {
base_src_compile
emake install_scripts || die
}
src_install() {
exeinto /usr/share/${P}/bin
find bin -type f -executable | xargs doexe || die
echo "PATH=\"/usr/share/${P}/bin\"" > "${S}/99${P}"
doenvd "${S}/99${P}" || die
dosym /usr/share/${P}/bin/RunAllPaths3G /usr/bin/RunAllPaths3G || die
insinto /usr/share/doc/${PF}
doins "${DISTDIR}/AllPathsV3_Manual_r1.0.docx"
}
^ permalink raw reply [flat|nested] 3+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-biology/allpaths: ChangeLog allpaths-3.1.ebuild
@ 2012-08-30 7:32 Justin Lecher (jlec)
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher (jlec) @ 2012-08-30 7:32 UTC (permalink / raw
To: gentoo-commits
jlec 12/08/30 07:32:21
Modified: ChangeLog allpaths-3.1.ebuild
Log:
sci-biology/allpaths: Fix for gcc-4.7
(Portage version: 2.2.0_alpha123/cvs/Linux x86_64)
Revision Changes Path
1.7 sci-biology/allpaths/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/allpaths/ChangeLog?rev=1.7&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/allpaths/ChangeLog?rev=1.7&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/allpaths/ChangeLog?r1=1.6&r2=1.7
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/allpaths/ChangeLog,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- ChangeLog 26 Jan 2010 20:43:21 -0000 1.6
+++ ChangeLog 30 Aug 2012 07:32:21 -0000 1.7
@@ -1,6 +1,10 @@
# ChangeLog for sci-biology/allpaths
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/ChangeLog,v 1.6 2010/01/26 20:43:21 weaver Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/ChangeLog,v 1.7 2012/08/30 07:32:21 jlec Exp $
+
+ 30 Aug 2012; Justin Lecher <jlec@gentoo.org> allpaths-3.1.ebuild,
+ +files/allpaths-3.1-gcc4.7.patch:
+ Fix for gcc-4.7
*allpaths-3.1 (26 Jan 2010)
1.2 sci-biology/allpaths/allpaths-3.1.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/allpaths/allpaths-3.1.ebuild?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/allpaths/allpaths-3.1.ebuild?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/allpaths/allpaths-3.1.ebuild?r1=1.1&r2=1.2
Index: allpaths-3.1.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/allpaths/allpaths-3.1.ebuild,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- allpaths-3.1.ebuild 26 Jan 2010 20:43:21 -0000 1.1
+++ allpaths-3.1.ebuild 30 Aug 2012 07:32:21 -0000 1.2
@@ -1,37 +1,39 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/allpaths-3.1.ebuild,v 1.1 2010/01/26 20:43:21 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/allpaths-3.1.ebuild,v 1.2 2012/08/30 07:32:21 jlec Exp $
-EAPI="2"
+EAPI=4
inherit base
DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
-SRC_URI="ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/allpaths-${PV}.tgz
+SRC_URI="
+ ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/allpaths-${PV}.tgz
ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/AllPathsV3_Manual_r1.0.docx"
LICENSE="Whitehead-MIT"
SLOT="3"
IUSE=""
-KEYWORDS="~amd64"
-
-DEPEND=">=sys-devel/gcc-4.3.2"
-RDEPEND=""
+KEYWORDS="~amd64 ~x86"
S="${WORKDIR}/AllPaths"
+PATCHES=( "${FILESDIR}"/${P}-gcc4.7.patch )
+
src_compile() {
base_src_compile
- emake install_scripts || die
+ emake install_scripts
}
src_install() {
- exeinto /usr/share/${P}/bin
+ exeinto /usr/libexec/${P}/
find bin -type f -executable | xargs doexe || die
- echo "PATH=\"/usr/share/${P}/bin\"" > "${S}/99${P}"
- doenvd "${S}/99${P}" || die
- dosym /usr/share/${P}/bin/RunAllPaths3G /usr/bin/RunAllPaths3G || die
- insinto /usr/share/doc/${PF}
- doins "${DISTDIR}/AllPathsV3_Manual_r1.0.docx"
+
+ echo "PATH=\"/usr/libexec/${P}/\"" > "${S}/50${P}"
+ doenvd "${S}/50${P}" || die
+
+ dosym /usr/libexec/${P}/RunAllPaths3G /usr/bin/RunAllPaths3G
+
+ dodoc "${DISTDIR}/AllPathsV3_Manual_r1.0.docx"
}
^ permalink raw reply [flat|nested] 3+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-biology/allpaths: ChangeLog allpaths-3.1.ebuild
@ 2012-08-30 7:46 Justin Lecher (jlec)
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher (jlec) @ 2012-08-30 7:46 UTC (permalink / raw
To: gentoo-commits
jlec 12/08/30 07:46:16
Modified: ChangeLog allpaths-3.1.ebuild
Log:
sci-biology/allpaths: Respect CXXFLAGS
(Portage version: 2.2.0_alpha123/cvs/Linux x86_64)
Revision Changes Path
1.8 sci-biology/allpaths/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/allpaths/ChangeLog?rev=1.8&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/allpaths/ChangeLog?rev=1.8&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/allpaths/ChangeLog?r1=1.7&r2=1.8
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/allpaths/ChangeLog,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- ChangeLog 30 Aug 2012 07:32:21 -0000 1.7
+++ ChangeLog 30 Aug 2012 07:46:16 -0000 1.8
@@ -1,6 +1,9 @@
# ChangeLog for sci-biology/allpaths
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/ChangeLog,v 1.7 2012/08/30 07:32:21 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/ChangeLog,v 1.8 2012/08/30 07:46:16 jlec Exp $
+
+ 30 Aug 2012; Justin Lecher <jlec@gentoo.org> allpaths-3.1.ebuild:
+ Respect CXXFLAGS
30 Aug 2012; Justin Lecher <jlec@gentoo.org> allpaths-3.1.ebuild,
+files/allpaths-3.1-gcc4.7.patch:
1.3 sci-biology/allpaths/allpaths-3.1.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/allpaths/allpaths-3.1.ebuild?rev=1.3&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/allpaths/allpaths-3.1.ebuild?rev=1.3&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/allpaths/allpaths-3.1.ebuild?r1=1.2&r2=1.3
Index: allpaths-3.1.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/allpaths/allpaths-3.1.ebuild,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- allpaths-3.1.ebuild 30 Aug 2012 07:32:21 -0000 1.2
+++ allpaths-3.1.ebuild 30 Aug 2012 07:46:16 -0000 1.3
@@ -1,6 +1,6 @@
# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/allpaths-3.1.ebuild,v 1.2 2012/08/30 07:32:21 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/allpaths-3.1.ebuild,v 1.3 2012/08/30 07:46:16 jlec Exp $
EAPI=4
@@ -21,6 +21,14 @@
PATCHES=( "${FILESDIR}"/${P}-gcc4.7.patch )
+src_prepare() {
+ sed \
+ -e "s:-O3:${CXXFLAGS}:g" \
+ -e 's:-ggdb3::g' \
+ -i Makefile* || die
+ base_src_prepare
+}
+
src_compile() {
base_src_compile
emake install_scripts
^ permalink raw reply [flat|nested] 3+ messages in thread
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2012-08-30 7:46 Justin Lecher (jlec)
2010-01-26 20:43 Andrey Kislyuk (weaver)
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