* [gentoo-commits] proj/sci:master commit in: sci-biology/allpathslg/
@ 2015-03-30 19:36 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2015-03-30 19:36 UTC (permalink / raw
To: gentoo-commits
commit: 1b6ab4256d7bcac9f54bac2ed2bb33dbb9183c24
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 30 19:36:20 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 30 19:36:20 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1b6ab425
sci-biology/allpathslg: version bump; added dependency on >=gcc-4.7
Package-Manager: portage-2.2.18
sci-biology/allpathslg/ChangeLog | 76 ++++++++++++++++++++++++++
sci-biology/allpathslg/allpathslg-52415.ebuild | 39 +++++++++++++
sci-biology/allpathslg/metadata.xml | 5 ++
3 files changed, 120 insertions(+)
diff --git a/sci-biology/allpathslg/ChangeLog b/sci-biology/allpathslg/ChangeLog
new file mode 100644
index 0000000..5e25459
--- /dev/null
+++ b/sci-biology/allpathslg/ChangeLog
@@ -0,0 +1,76 @@
+# ChangeLog for sci-biology/allpathslg
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpathslg/ChangeLog,v 1.16 2013/11/13 02:34:46 patrick Exp $
+
+ 13 Nov 2013; Patrick Lauer <patrick@gentoo.org> allpathslg-42337.ebuild,
+ allpathslg-47093.ebuild:
+ Removing x86 keyword as dependency sci-biology/vaal does not work on x86
+
+*allpathslg-47093 (17 Jul 2013)
+
+ 17 Jul 2013; Justin Lecher <jlec@gentoo.org> allpathslg-42337.ebuild,
+ +allpathslg-47093.ebuild:
+ Version Bump
+
+ 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
+ Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
+
+ 20 Feb 2013; Justin Lecher <jlec@gentoo.org> -allpathslg-37578.ebuild:
+ Drop old
+
+ 20 Feb 2013; Agostino Sarubbo <ago@gentoo.org> allpathslg-42337.ebuild:
+ Stable for amd64, wrt bug #458106
+
+ 18 Feb 2013; Justin Lecher <jlec@gentoo.org> -allpathslg-41839.ebuild,
+ metadata.xml:
+ Drop old
+
+ 14 Dec 2012; Ulrich Müller <ulm@gentoo.org> allpathslg-37578.ebuild,
+ allpathslg-41839.ebuild, allpathslg-42337.ebuild:
+ Fix LICENSE, MIT (Expat) according to COPYING file.
+
+ 19 Nov 2012; Justin Lecher <jlec@gentoo.org> allpathslg-37578.ebuild,
+ allpathslg-41839.ebuild, allpathslg-42337.ebuild:
+ Block sci-biology/allpaths due to file collision, #443740
+
+*allpathslg-42337 (09 Jul 2012)
+
+ 09 Jul 2012; Justin Lecher <jlec@gentoo.org> +allpathslg-42337.ebuild:
+ Version bump, fix compilation errors with gcc-4.7, #425472
+
+*allpathslg-41839 (29 May 2012)
+
+ 29 May 2012; Andrey Kislyuk <weaver@gentoo.org> -allpathslg-38573.ebuild,
+ -allpathslg-40063.ebuild, +allpathslg-41839.ebuild:
+ version bump
+
+*allpathslg-40063 (28 Dec 2011)
+
+ 28 Dec 2011; Andrey Kislyuk <weaver@gentoo.org>
+ -allpathslg-35725-r1.ebuild, +allpathslg-40063.ebuild:
+ Version bump, remove old
+
+ 15 Oct 2011; Markos Chandras <hwoarang@gentoo.org> allpathslg-37578.ebuild:
+ Stable on amd64 wrt bug #384379
+
+*allpathslg-38573 (25 Sep 2011)
+
+ 25 Sep 2011; Andrey Kislyuk <weaver@gentoo.org> +allpathslg-38573.ebuild:
+ Version bump
+
+*allpathslg-37578 (20 Jun 2011)
+
+ 20 Jun 2011; Andrey Kislyuk <weaver@gentoo.org> +allpathslg-37578.ebuild:
+ Version bump
+
+*allpathslg-35725-r1 (27 Jan 2011)
+
+ 27 Jan 2011; Andrey Kislyuk <weaver@gentoo.org> -allpathslg-35725.ebuild,
+ +allpathslg-35725-r1.ebuild:
+ Drop ~x86, avoid collision with sci-biology/vaal
+
+*allpathslg-35725 (25 Jan 2011)
+
+ 25 Jan 2011; Andrey Kislyuk <weaver@gentoo.org> +allpathslg-35725.ebuild,
+ +metadata.xml:
+ Package move from sci-biology/allpaths and version bump
diff --git a/sci-biology/allpathslg/allpathslg-52415.ebuild b/sci-biology/allpathslg/allpathslg-52415.ebuild
new file mode 100644
index 0000000..8750b5f
--- /dev/null
+++ b/sci-biology/allpathslg/allpathslg-52415.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpathslg/allpathslg-42337.ebuild,v 1.6 2013/11/13 02:34:46 patrick Exp $
+
+EAPI=4
+
+inherit autotools flag-o-matic
+
+DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
+HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
+SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64"
+
+# as of release 44849, GCC 4.7.0 (or higher) is required
+# seems pre gcc-4.7 users must stay with:
+# ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-01/allpathslg-44837.tar.gz
+DEPEND="
+ >=sys-devel/gcc-4.7
+ dev-libs/boost
+ !sci-biology/allpaths
+ sci-biology/vaal"
+RDEPEND=""
+
+src_prepare() {
+ sed -i 's/-ggdb3//' configure.ac || die
+ eautoreconf
+}
+
+src_install() {
+ einstall || die
+ # Provided by sci-biology/vaal
+ for i in QueryLookupTable ScaffoldAccuracy MakeLookupTable Fastb ShortQueryLookup; do
+ rm "${D}/usr/bin/$i" || die
+ done
+}
diff --git a/sci-biology/allpathslg/metadata.xml b/sci-biology/allpathslg/metadata.xml
new file mode 100644
index 0000000..f17a827
--- /dev/null
+++ b/sci-biology/allpathslg/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>
^ permalink raw reply related [flat|nested] 3+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/allpathslg/
@ 2015-03-30 19:45 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2015-03-30 19:45 UTC (permalink / raw
To: gentoo-commits
commit: 461e6b39d6ca6b02f0feb37821e4ca65934e619d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 30 19:44:47 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 30 19:44:47 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=461e6b39
sci-biology/allpathslg: noted another home-like web page
Package-Manager: portage-2.2.18
sci-biology/allpathslg/ChangeLog | 6 +++++-
sci-biology/allpathslg/allpathslg-52415.ebuild | 1 +
2 files changed, 6 insertions(+), 1 deletion(-)
diff --git a/sci-biology/allpathslg/ChangeLog b/sci-biology/allpathslg/ChangeLog
index 5e25459..41ef438 100644
--- a/sci-biology/allpathslg/ChangeLog
+++ b/sci-biology/allpathslg/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/allpathslg
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpathslg/ChangeLog,v 1.16 2013/11/13 02:34:46 patrick Exp $
+ 30 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ allpathslg-52415.ebuild:
+ sci-biology/allpathslg: noted another home-like web page
+
13 Nov 2013; Patrick Lauer <patrick@gentoo.org> allpathslg-42337.ebuild,
allpathslg-47093.ebuild:
Removing x86 keyword as dependency sci-biology/vaal does not work on x86
diff --git a/sci-biology/allpathslg/allpathslg-52415.ebuild b/sci-biology/allpathslg/allpathslg-52415.ebuild
index 8750b5f..ff7bdca 100644
--- a/sci-biology/allpathslg/allpathslg-52415.ebuild
+++ b/sci-biology/allpathslg/allpathslg-52415.ebuild
@@ -7,6 +7,7 @@ EAPI=4
inherit autotools flag-o-matic
DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
+# see also http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12
HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz"
^ permalink raw reply related [flat|nested] 3+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/allpathslg/
@ 2015-04-02 10:15 Justin Lecher
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher @ 2015-04-02 10:15 UTC (permalink / raw
To: gentoo-commits
commit: a9c81628eca87f9cc79d8441dce83f7f0e9d68fd
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 31 10:52:01 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Apr 1 06:16:35 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a9c81628
Moved to tree
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/allpathslg/ChangeLog | 80 --------------------------
sci-biology/allpathslg/allpathslg-52415.ebuild | 40 -------------
sci-biology/allpathslg/metadata.xml | 5 --
3 files changed, 125 deletions(-)
diff --git a/sci-biology/allpathslg/ChangeLog b/sci-biology/allpathslg/ChangeLog
deleted file mode 100644
index 41ef438..0000000
--- a/sci-biology/allpathslg/ChangeLog
+++ /dev/null
@@ -1,80 +0,0 @@
-# ChangeLog for sci-biology/allpathslg
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpathslg/ChangeLog,v 1.16 2013/11/13 02:34:46 patrick Exp $
-
- 30 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- allpathslg-52415.ebuild:
- sci-biology/allpathslg: noted another home-like web page
-
- 13 Nov 2013; Patrick Lauer <patrick@gentoo.org> allpathslg-42337.ebuild,
- allpathslg-47093.ebuild:
- Removing x86 keyword as dependency sci-biology/vaal does not work on x86
-
-*allpathslg-47093 (17 Jul 2013)
-
- 17 Jul 2013; Justin Lecher <jlec@gentoo.org> allpathslg-42337.ebuild,
- +allpathslg-47093.ebuild:
- Version Bump
-
- 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
- Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
-
- 20 Feb 2013; Justin Lecher <jlec@gentoo.org> -allpathslg-37578.ebuild:
- Drop old
-
- 20 Feb 2013; Agostino Sarubbo <ago@gentoo.org> allpathslg-42337.ebuild:
- Stable for amd64, wrt bug #458106
-
- 18 Feb 2013; Justin Lecher <jlec@gentoo.org> -allpathslg-41839.ebuild,
- metadata.xml:
- Drop old
-
- 14 Dec 2012; Ulrich Müller <ulm@gentoo.org> allpathslg-37578.ebuild,
- allpathslg-41839.ebuild, allpathslg-42337.ebuild:
- Fix LICENSE, MIT (Expat) according to COPYING file.
-
- 19 Nov 2012; Justin Lecher <jlec@gentoo.org> allpathslg-37578.ebuild,
- allpathslg-41839.ebuild, allpathslg-42337.ebuild:
- Block sci-biology/allpaths due to file collision, #443740
-
-*allpathslg-42337 (09 Jul 2012)
-
- 09 Jul 2012; Justin Lecher <jlec@gentoo.org> +allpathslg-42337.ebuild:
- Version bump, fix compilation errors with gcc-4.7, #425472
-
-*allpathslg-41839 (29 May 2012)
-
- 29 May 2012; Andrey Kislyuk <weaver@gentoo.org> -allpathslg-38573.ebuild,
- -allpathslg-40063.ebuild, +allpathslg-41839.ebuild:
- version bump
-
-*allpathslg-40063 (28 Dec 2011)
-
- 28 Dec 2011; Andrey Kislyuk <weaver@gentoo.org>
- -allpathslg-35725-r1.ebuild, +allpathslg-40063.ebuild:
- Version bump, remove old
-
- 15 Oct 2011; Markos Chandras <hwoarang@gentoo.org> allpathslg-37578.ebuild:
- Stable on amd64 wrt bug #384379
-
-*allpathslg-38573 (25 Sep 2011)
-
- 25 Sep 2011; Andrey Kislyuk <weaver@gentoo.org> +allpathslg-38573.ebuild:
- Version bump
-
-*allpathslg-37578 (20 Jun 2011)
-
- 20 Jun 2011; Andrey Kislyuk <weaver@gentoo.org> +allpathslg-37578.ebuild:
- Version bump
-
-*allpathslg-35725-r1 (27 Jan 2011)
-
- 27 Jan 2011; Andrey Kislyuk <weaver@gentoo.org> -allpathslg-35725.ebuild,
- +allpathslg-35725-r1.ebuild:
- Drop ~x86, avoid collision with sci-biology/vaal
-
-*allpathslg-35725 (25 Jan 2011)
-
- 25 Jan 2011; Andrey Kislyuk <weaver@gentoo.org> +allpathslg-35725.ebuild,
- +metadata.xml:
- Package move from sci-biology/allpaths and version bump
diff --git a/sci-biology/allpathslg/allpathslg-52415.ebuild b/sci-biology/allpathslg/allpathslg-52415.ebuild
deleted file mode 100644
index ff7bdca..0000000
--- a/sci-biology/allpathslg/allpathslg-52415.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpathslg/allpathslg-42337.ebuild,v 1.6 2013/11/13 02:34:46 patrick Exp $
-
-EAPI=4
-
-inherit autotools flag-o-matic
-
-DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
-# see also http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12
-HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
-SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64"
-
-# as of release 44849, GCC 4.7.0 (or higher) is required
-# seems pre gcc-4.7 users must stay with:
-# ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-01/allpathslg-44837.tar.gz
-DEPEND="
- >=sys-devel/gcc-4.7
- dev-libs/boost
- !sci-biology/allpaths
- sci-biology/vaal"
-RDEPEND=""
-
-src_prepare() {
- sed -i 's/-ggdb3//' configure.ac || die
- eautoreconf
-}
-
-src_install() {
- einstall || die
- # Provided by sci-biology/vaal
- for i in QueryLookupTable ScaffoldAccuracy MakeLookupTable Fastb ShortQueryLookup; do
- rm "${D}/usr/bin/$i" || die
- done
-}
diff --git a/sci-biology/allpathslg/metadata.xml b/sci-biology/allpathslg/metadata.xml
deleted file mode 100644
index f17a827..0000000
--- a/sci-biology/allpathslg/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <herd>sci-biology</herd>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 3+ messages in thread
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2015-03-30 19:36 [gentoo-commits] proj/sci:master commit in: sci-biology/allpathslg/ Martin Mokrejs
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2015-03-30 19:45 Martin Mokrejs
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