[gentoo-commits] proj/sci:master commit in: sci-biology/tophat/

[Martin Mokrejs]

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@×××××××××××××××.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@×××××××××××××××.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 )