* [gentoo-commits] proj/sci:master commit in: sci-biology/tophat/
@ 2015-04-28 19:04 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2015-04-28 19:04 UTC (permalink / raw
To: gentoo-commits
commit: da3ce5959e5b2a9575a88703a004ed6172e3b31c
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Apr 28 19:04:22 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Apr 28 19:04:22 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=da3ce595
sci-biology/tophat: recorded depependencies; dropped KEYWORDS until we have slotted samtools (or multiple static binaries with version appended to filename), link tophat_reporter against -lsam-0.1.18 and similarly adjust tophat_reporter
Package-Manager: portage-2.2.18
sci-biology/tophat/ChangeLog | 7 +++++++
sci-biology/tophat/tophat-2.0.12.ebuild | 17 ++++++++++++++---
sci-biology/tophat/tophat-2.0.13.ebuild | 17 +++++++++++++----
sci-biology/tophat/tophat-2.0.14.ebuild | 16 ++++++++++++----
4 files changed, 46 insertions(+), 11 deletions(-)
diff --git a/sci-biology/tophat/ChangeLog b/sci-biology/tophat/ChangeLog
index 6339ca9..62520a2 100644
--- a/sci-biology/tophat/ChangeLog
+++ b/sci-biology/tophat/ChangeLog
@@ -3,6 +3,13 @@
# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/ChangeLog,v 1.14 2015/04/07 14:35:24 jlec Exp $
28 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ tophat-2.0.12.ebuild, tophat-2.0.13.ebuild, tophat-2.0.14.ebuild:
+ sci-biology/tophat: recorded depependencies; dropped KEYWORDS until we have
+ slotted samtools (or multiple static binaries with version appended to
+ filename), link tophat_reporter against -lsam-0.1.18 and similarly adjust
+ tophat_reporter
+
+ 28 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
tophat-2.0.14.ebuild:
sci-biology/tophat: try to introduce all-recursive target to make upstream
'make all' call happy
diff --git a/sci-biology/tophat/tophat-2.0.12.ebuild b/sci-biology/tophat/tophat-2.0.12.ebuild
index f5f059d..13bb0f4 100644
--- a/sci-biology/tophat/tophat-2.0.12.ebuild
+++ b/sci-biology/tophat/tophat-2.0.12.ebuild
@@ -9,7 +9,7 @@ PYTHON_COMPAT=( python2_7 )
inherit autotools-utils python-single-r1
-DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
+DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie/bowtie2"
HOMEPAGE="http://ccb.jhu.edu/software/tophat"
# https://github.com/infphilo/tophat
# http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.14.tar.gz
@@ -17,13 +17,21 @@ SRC_URI="http://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz"
LICENSE="Artistic"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
IUSE="debug"
DEPEND="dev-libs/boost"
# sci-biology/seqan provides binaries and headers but there are no *.so files so no need for a runtime dependency
+# boost and seqan is needed for tophat_reporter
+
+# tophat.py calls
+# samtools_0.1.18 view -h -
+# samtools_0.1.18 sort
+# samtools_0.1.18 merge -f -h -u -Q --sam-header
RDEPEND="${DEPEND}
- <=sci-biology/bowtie-2.2.3"
+ >=sci-biology/samtools-0.1.17
+ <=sci-biology/samtools-0.1.19
+ >=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5 <=sci-biology/bowtie-2.2.3 )"
# PATCHES=( "${FILESDIR}"/${P}-flags.patch )
@@ -31,6 +39,7 @@ src_prepare() {
sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i configure* Makefile* src/Makefile* || die
sed -e "s#./SeqAn-1.3#"${S}"/src/SeqAn-1.3#g" -i configure* || die
#rm -rf src/SeqAn* || die
+ eautoreconf
autotools-utils_src_prepare
}
@@ -44,6 +53,8 @@ src_configure() {
}
src_install() {
+ # introduce empty all-recursive: target in tophat-2.0.14_build/src/Makefile (BUG: does not replace?)
+ sed -e "s#^all: all-am#all: all-am\nall-recursive: all#g" -i src/Makefile* || die
autotools-utils_src_install
python_fix_shebang "${ED}"/usr/bin/tophat
}
diff --git a/sci-biology/tophat/tophat-2.0.13.ebuild b/sci-biology/tophat/tophat-2.0.13.ebuild
index 5e56cc4..6d4cdcb 100644
--- a/sci-biology/tophat/tophat-2.0.13.ebuild
+++ b/sci-biology/tophat/tophat-2.0.13.ebuild
@@ -9,7 +9,7 @@ PYTHON_COMPAT=( python2_7 )
inherit autotools-utils python-single-r1
-DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
+DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie/bowtie2"
HOMEPAGE="http://ccb.jhu.edu/software/tophat"
# https://github.com/infphilo/tophat
# http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.14.tar.gz
@@ -17,14 +17,21 @@ SRC_URI="http://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz"
LICENSE="Artistic"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
IUSE="debug"
DEPEND="dev-libs/boost"
-# >=sci-biology/tophat-2.0.13 contain bundled samtools-0.1.18 and SeqAn-1.3
# sci-biology/seqan provides binaries and headers but there are no *.so files so no need for a runtime dependency
+# boost and seqan is needed for tophat_reporter
+
+# tophat.py calls
+# samtools_0.1.18 view -h -
+# samtools_0.1.18 sort
+# samtools_0.1.18 merge -f -h -u -Q --sam-header
RDEPEND="${DEPEND}
- <=sci-biology/bowtie-2.2.3"
+ >=sci-biology/samtools-0.1.17
+ <=sci-biology/samtools-0.1.19
+ >=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5 <=sci-biology/bowtie-2.2.3 )"
# PATCHES=( "${FILESDIR}"/${P}-flags.patch )
@@ -49,6 +56,8 @@ src_configure() {
}
src_install() {
+ # introduce empty all-recursive: target in tophat-2.0.14_build/src/Makefile (BUG: does not replace?)
+ sed -e "s#^all: all-am#all: all-am\nall-recursive: all#g" -i src/Makefile* || die
autotools-utils_src_install
python_fix_shebang "${ED}"/usr/bin/tophat
}
diff --git a/sci-biology/tophat/tophat-2.0.14.ebuild b/sci-biology/tophat/tophat-2.0.14.ebuild
index 1e48d7d..2091866 100644
--- a/sci-biology/tophat/tophat-2.0.14.ebuild
+++ b/sci-biology/tophat/tophat-2.0.14.ebuild
@@ -9,7 +9,7 @@ PYTHON_COMPAT=( python2_7 )
inherit autotools-utils python-single-r1
-DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
+DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie/bowtie2"
HOMEPAGE="http://ccb.jhu.edu/software/tophat"
# https://github.com/infphilo/tophat
# http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.14.tar.gz
@@ -17,14 +17,22 @@ SRC_URI="http://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz"
LICENSE="Artistic"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
IUSE="debug"
DEPEND="dev-libs/boost"
-# >=sci-biology/tophat-2.0.13 contains bundled samtools-0.1.18 and SeqAn-1.3
# sci-biology/seqan provides binaries and headers but there are no *.so files so no need for a runtime dependency
+# boost and seqan is needed for tophat_reporter
+
+# tophat.py calls
+# samtools_0.1.18 view -h -
+# samtools_0.1.18 sort
+# samtools_0.1.18 merge -f -h -u -Q --sam-header
RDEPEND="${DEPEND}
- <=sci-biology/bowtie-2.2.3"
+ >=sci-biology/samtools-0.1.17
+ <=sci-biology/samtools-0.1.19
+ >=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5 <=sci-biology/bowtie-2.2.3 )"
+
# see https://aur.archlinux.org/packages/tophat/ about linking issues
# PATCHES=( "${FILESDIR}"/${P}-flags.patch )
^ permalink raw reply related [flat|nested] 5+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/tophat/
@ 2015-09-07 6:49 Justin Lecher
0 siblings, 0 replies; 5+ messages in thread
From: Justin Lecher @ 2015-09-07 6:49 UTC (permalink / raw
To: gentoo-commits
commit: e8bad311842f4dbbd58670dc3dd9a778258fae25
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 7 06:49:23 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 7 06:49:23 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e8bad311
sci-biology/tophat: Drop unnecessary deps
On behalf of Martin Mokrejs
Package-Manager: portage-2.2.20.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/tophat/metadata.xml | 3 ---
sci-biology/tophat/tophat-2.0.12.ebuild | 2 --
sci-biology/tophat/tophat-2.0.13.ebuild | 2 --
sci-biology/tophat/tophat-2.0.14.ebuild | 2 --
4 files changed, 9 deletions(-)
diff --git a/sci-biology/tophat/metadata.xml b/sci-biology/tophat/metadata.xml
index 36cf4a1..f17a827 100644
--- a/sci-biology/tophat/metadata.xml
+++ b/sci-biology/tophat/metadata.xml
@@ -2,7 +2,4 @@
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
- <use>
- <flag name="bam">Compile support for the BAM format</flag>
- </use>
</pkgmetadata>
diff --git a/sci-biology/tophat/tophat-2.0.12.ebuild b/sci-biology/tophat/tophat-2.0.12.ebuild
index 119418e..7c9cf07 100644
--- a/sci-biology/tophat/tophat-2.0.12.ebuild
+++ b/sci-biology/tophat/tophat-2.0.12.ebuild
@@ -29,8 +29,6 @@ DEPEND="dev-libs/boost"
# samtools_0.1.18 sort
# samtools_0.1.18 merge -f -h -u -Q --sam-header
RDEPEND="${DEPEND}
- >=sci-biology/samtools-0.1.17[${PYTHON_USEDEP}]
- <=sci-biology/samtools-0.1.19[${PYTHON_USEDEP}]
>=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5 <=sci-biology/bowtie-2.2.3 )"
# PATCHES=( "${FILESDIR}"/${P}-flags.patch )
diff --git a/sci-biology/tophat/tophat-2.0.13.ebuild b/sci-biology/tophat/tophat-2.0.13.ebuild
index 88e26be..6625162 100644
--- a/sci-biology/tophat/tophat-2.0.13.ebuild
+++ b/sci-biology/tophat/tophat-2.0.13.ebuild
@@ -29,8 +29,6 @@ DEPEND="dev-libs/boost"
# samtools_0.1.18 sort
# samtools_0.1.18 merge -f -h -u -Q --sam-header
RDEPEND="${DEPEND}
- >=sci-biology/samtools-0.1.17[${PYTHON_USEDEP}]
- <=sci-biology/samtools-0.1.19[${PYTHON_USEDEP}]
>=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5 <=sci-biology/bowtie-2.2.3 )"
# PATCHES=( "${FILESDIR}"/${P}-flags.patch )
diff --git a/sci-biology/tophat/tophat-2.0.14.ebuild b/sci-biology/tophat/tophat-2.0.14.ebuild
index f38855b..0b8f1e8 100644
--- a/sci-biology/tophat/tophat-2.0.14.ebuild
+++ b/sci-biology/tophat/tophat-2.0.14.ebuild
@@ -29,8 +29,6 @@ DEPEND="dev-libs/boost"
# samtools_0.1.18 sort
# samtools_0.1.18 merge -f -h -u -Q --sam-header
RDEPEND="${DEPEND}
- >=sci-biology/samtools-0.1.17[${PYTHON_USEDEP}]
- <=sci-biology/samtools-0.1.19[${PYTHON_USEDEP}]
>=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5 <=sci-biology/bowtie-2.2.3 )"
# see https://aur.archlinux.org/packages/tophat/ about linking issues
^ permalink raw reply related [flat|nested] 5+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/tophat/
@ 2015-08-15 6:07 Justin Lecher
0 siblings, 0 replies; 5+ messages in thread
From: Justin Lecher @ 2015-08-15 6:07 UTC (permalink / raw
To: gentoo-commits
commit: c18359435de9e9cb23bcfaefd6ff9ad502ab2f92
Author: layman <layman <AT> localhost>
AuthorDate: Fri Aug 14 21:06:49 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Aug 14 21:08:47 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c1835943
sci-biology/tophat: tophat-2.1.0 version bump
Package-Manager: portage-2.2.20-prefix
sci-biology/tophat/ChangeLog | 5 ++++
sci-biology/tophat/tophat-2.1.0.ebuild | 43 ++++++++++++++++++++++++++++++++++
2 files changed, 48 insertions(+)
diff --git a/sci-biology/tophat/ChangeLog b/sci-biology/tophat/ChangeLog
index 84e8313..93ca57b 100644
--- a/sci-biology/tophat/ChangeLog
+++ b/sci-biology/tophat/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/ChangeLog,v 1.14 2015/04/07 14:35:24 jlec Exp $
+*tophat-2.1.0 (14 Aug 2015)
+
+ 14 Aug 2015; Michael Schubert <mschu.dev@gmail.com> +tophat-2.1.0.ebuild:
+ sci-biology/tophat: tophat-2.1.0 version bump
+
02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
tophat-2.0.12.ebuild, tophat-2.0.13.ebuild, tophat-2.0.14.ebuild:
added PYTHON_USEDEP
diff --git a/sci-biology/tophat/tophat-2.1.0.ebuild b/sci-biology/tophat/tophat-2.1.0.ebuild
new file mode 100644
index 0000000..0e4b31e
--- /dev/null
+++ b/sci-biology/tophat/tophat-2.1.0.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/tophat-2.0.9.ebuild,v 1.1 2014/03/06 09:46:50 jlec Exp $
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=yes
+AUTOTOOLS_IN_SOURCE_BUILD=yes
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools-utils python-single-r1
+
+DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie/bowtie2"
+HOMEPAGE="http://ccb.jhu.edu/software/tophat"
+SRC_URI="https://github.com/infphilo/tophat/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS=""
+IUSE="debug"
+
+DEPEND="dev-libs/boost"
+# sci-biology/seqan provides binaries and headers but there are no *.so files so no need for a runtime dependency
+# boost and seqan is needed for tophat_reporter
+
+# tophat.py calls
+# samtools_0.1.18 view -h -
+# samtools_0.1.18 sort
+# samtools_0.1.18 merge -f -h -u -Q --sam-header
+RDEPEND="${DEPEND}
+ >=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5 <=sci-biology/bowtie-2.2.3 )"
+
+src_configure() {
+ local myeconfargs=(
+ $(use_enable debug)
+ )
+ autotools-utils_src_configure
+
+ echo "../src/libtophat.a: libtophat.a" >> src/Makefile
+ echo "../src/libgc.a: libgc.a" >> src/Makefile
+ echo "samtools_0.1.18:" >> src/Makefile
+ echo -e "\tcp samtools-0.1.18/\$@ \$@" >> src/Makefile
+}
^ permalink raw reply related [flat|nested] 5+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/tophat/
@ 2015-05-02 16:29 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2015-05-02 16:29 UTC (permalink / raw
To: gentoo-commits
commit: 74bc48aaac3968150d9dbcc52877289811171493
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat May 2 16:12:45 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat May 2 16:12:45 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=74bc48aa
added PYTHON_USEDEP
Package-Manager: portage-2.2.18
sci-biology/tophat/ChangeLog | 4 ++++
sci-biology/tophat/tophat-2.0.12.ebuild | 4 ++--
sci-biology/tophat/tophat-2.0.13.ebuild | 4 ++--
sci-biology/tophat/tophat-2.0.14.ebuild | 4 ++--
4 files changed, 10 insertions(+), 6 deletions(-)
diff --git a/sci-biology/tophat/ChangeLog b/sci-biology/tophat/ChangeLog
index 62520a2..84e8313 100644
--- a/sci-biology/tophat/ChangeLog
+++ b/sci-biology/tophat/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/ChangeLog,v 1.14 2015/04/07 14:35:24 jlec Exp $
+ 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ tophat-2.0.12.ebuild, tophat-2.0.13.ebuild, tophat-2.0.14.ebuild:
+ added PYTHON_USEDEP
+
28 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
tophat-2.0.12.ebuild, tophat-2.0.13.ebuild, tophat-2.0.14.ebuild:
sci-biology/tophat: recorded depependencies; dropped KEYWORDS until we have
diff --git a/sci-biology/tophat/tophat-2.0.12.ebuild b/sci-biology/tophat/tophat-2.0.12.ebuild
index 13bb0f4..f818f1c 100644
--- a/sci-biology/tophat/tophat-2.0.12.ebuild
+++ b/sci-biology/tophat/tophat-2.0.12.ebuild
@@ -29,8 +29,8 @@ DEPEND="dev-libs/boost"
# samtools_0.1.18 sort
# samtools_0.1.18 merge -f -h -u -Q --sam-header
RDEPEND="${DEPEND}
- >=sci-biology/samtools-0.1.17
- <=sci-biology/samtools-0.1.19
+ >=sci-biology/samtools-0.1.17[${PYTHON_USEDEP}]
+ <=sci-biology/samtools-0.1.19[${PYTHON_USEDEP}]
>=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5 <=sci-biology/bowtie-2.2.3 )"
# PATCHES=( "${FILESDIR}"/${P}-flags.patch )
diff --git a/sci-biology/tophat/tophat-2.0.13.ebuild b/sci-biology/tophat/tophat-2.0.13.ebuild
index 6d4cdcb..c24d230 100644
--- a/sci-biology/tophat/tophat-2.0.13.ebuild
+++ b/sci-biology/tophat/tophat-2.0.13.ebuild
@@ -29,8 +29,8 @@ DEPEND="dev-libs/boost"
# samtools_0.1.18 sort
# samtools_0.1.18 merge -f -h -u -Q --sam-header
RDEPEND="${DEPEND}
- >=sci-biology/samtools-0.1.17
- <=sci-biology/samtools-0.1.19
+ >=sci-biology/samtools-0.1.17[${PYTHON_USEDEP}]
+ <=sci-biology/samtools-0.1.19[${PYTHON_USEDEP}]
>=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5 <=sci-biology/bowtie-2.2.3 )"
# PATCHES=( "${FILESDIR}"/${P}-flags.patch )
diff --git a/sci-biology/tophat/tophat-2.0.14.ebuild b/sci-biology/tophat/tophat-2.0.14.ebuild
index 2091866..579641f 100644
--- a/sci-biology/tophat/tophat-2.0.14.ebuild
+++ b/sci-biology/tophat/tophat-2.0.14.ebuild
@@ -29,8 +29,8 @@ DEPEND="dev-libs/boost"
# samtools_0.1.18 sort
# samtools_0.1.18 merge -f -h -u -Q --sam-header
RDEPEND="${DEPEND}
- >=sci-biology/samtools-0.1.17
- <=sci-biology/samtools-0.1.19
+ >=sci-biology/samtools-0.1.17[${PYTHON_USEDEP}]
+ <=sci-biology/samtools-0.1.19[${PYTHON_USEDEP}]
>=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5 <=sci-biology/bowtie-2.2.3 )"
# see https://aur.archlinux.org/packages/tophat/ about linking issues
^ permalink raw reply related [flat|nested] 5+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/tophat/
@ 2015-04-28 12:54 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2015-04-28 12:54 UTC (permalink / raw
To: gentoo-commits
commit: 5cbf89b2f0459c333ffae9e526a95e40931137b4
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Apr 28 12:53:31 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Apr 28 12:53:31 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5cbf89b2
sci-biology/tophat: try to introduce all-recursive target to make upstream 'make all' call happy
Package-Manager: portage-2.2.18
sci-biology/tophat/ChangeLog | 8 ++++++--
sci-biology/tophat/tophat-2.0.14.ebuild | 2 ++
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/sci-biology/tophat/ChangeLog b/sci-biology/tophat/ChangeLog
index a262a0b..6339ca9 100644
--- a/sci-biology/tophat/ChangeLog
+++ b/sci-biology/tophat/ChangeLog
@@ -1,7 +1,12 @@
# ChangeLog for sci-biology/tophat
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/ChangeLog,v 1.14 2015/04/07 14:35:24 jlec Exp $
+ 28 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ tophat-2.0.14.ebuild:
+ sci-biology/tophat: try to introduce all-recursive target to make upstream
+ 'make all' call happy
+
17 Oct 2014; Sergey Popov <pinkbyte@gentoo.org> tophat-1.0.12.ebuild:
Non-maintainer commit: fix building, approved by Justin Lecher
@@ -66,4 +71,3 @@
07 Dec 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml,
+tophat-1.0.12.ebuild:
Import from Science overlay and version bump. Thanks to Philippe Veber.
-
diff --git a/sci-biology/tophat/tophat-2.0.14.ebuild b/sci-biology/tophat/tophat-2.0.14.ebuild
index 09b7ce8..1e48d7d 100644
--- a/sci-biology/tophat/tophat-2.0.14.ebuild
+++ b/sci-biology/tophat/tophat-2.0.14.ebuild
@@ -49,6 +49,8 @@ src_configure() {
}
src_install() {
+ # introduce empty all-recursive: target in tophat-2.0.14_build/src/Makefile (BUG: does not replace?)
+ sed -e "s#^all: all-am#all: all-am\nall-recursive: all#g" -i src/Makefile* || die
autotools-utils_src_install
python_fix_shebang "${ED}"/usr/bin/tophat
}
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