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 <[email protected]> + 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 <[email protected]> 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 )
