commit: ece13202e880ee4219486309af8c82ff738b915d Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Mon Apr 27 11:09:07 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Mon Apr 27 11:09:07 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ece13202
sci-biology/tophat: version bumps; we can use the bundled SeqAn-1.3 and also the samtools-0.1.18, it is just for compilation AFAIK; note also the specific version of bowtie (I infer <= versions are supported only) Package-Manager: portage-2.2.18 sci-biology/tophat/ChangeLog | 69 ++++++++++++++ sci-biology/tophat/files/tophat-2.0.9-flags.patch | 109 ++++++++++++++++++++++ sci-biology/tophat/metadata.xml | 8 ++ sci-biology/tophat/tophat-2.0.12.ebuild | 49 ++++++++++ sci-biology/tophat/tophat-2.0.13.ebuild | 54 +++++++++++ sci-biology/tophat/tophat-2.0.14.ebuild | 54 +++++++++++ 6 files changed, 343 insertions(+) diff --git a/sci-biology/tophat/ChangeLog b/sci-biology/tophat/ChangeLog new file mode 100644 index 0000000..a262a0b --- /dev/null +++ b/sci-biology/tophat/ChangeLog @@ -0,0 +1,69 @@ +# ChangeLog for sci-biology/tophat +# Copyright 1999-2014 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 $ + + 17 Oct 2014; Sergey Popov <[email protected]> tophat-1.0.12.ebuild: + Non-maintainer commit: fix building, approved by Justin Lecher + +*tophat-2.0.9 (06 Mar 2014) + + 06 Mar 2014; Justin Lecher <[email protected]> +tophat-2.0.9.ebuild, + +files/tophat-2.0.9-flags.patch: + Version Bump, #502532; thanks José María Fernández González for the new + ebuild + +*tophat-2.0.8 (13 Mar 2013) + + 13 Mar 2013; Justin Lecher <[email protected]> +tophat-2.0.8.ebuild, + +files/tophat-2.0.8-flags.patch: + Version Bump; unbundle sci-biology/seqan + + 12 Mar 2013; Justin Lecher <[email protected]> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*tophat-2.0.2 (19 Jul 2012) + + 19 Jul 2012; Justin Lecher <[email protected]> tophat-2.0.0.ebuild, + +tophat-2.0.2.ebuild, +files/tophat-2.0.2-flags.patch, metadata.xml: + Version Bump; do parallel builds; handle debug build + + 25 Apr 2012; Justin Lecher <[email protected]> tophat-1.0.12.ebuild, + tophat-1.4.1.ebuild, tophat-2.0.0.ebuild: + Drop unnessecary die + +*tophat-2.0.0 (15 Apr 2012) + + 15 Apr 2012; Andrey Kislyuk <[email protected]> -tophat-1.3.3.ebuild, + +tophat-2.0.0.ebuild: + version bump + +*tophat-1.4.1 (04 Feb 2012) +*tophat-1.3.3 (04 Feb 2012) + + 04 Feb 2012; Andrey Kislyuk <[email protected]> -tophat-1.3.2.ebuild, + +tophat-1.3.3.ebuild, +tophat-1.4.1.ebuild: + version bump + + 04 Feb 2012; Andrey Kislyuk <[email protected]> tophat-1.3.2.ebuild: + filter as-needed + +*tophat-1.3.2 (26 Sep 2011) + + 26 Sep 2011; Andrey Kislyuk <[email protected]> +tophat-1.3.2.ebuild: + Version bump + + 05 Apr 2010; Pawel Hajdan jr <[email protected]> tophat-1.0.12.ebuild: + x86 stable wrt bug #311829 + + 29 Mar 2010; Pacho Ramos <[email protected]> tophat-1.0.12.ebuild: + amd64 stable, bug 311829 + + 07 Dec 2009; Andrey Kislyuk <[email protected]> tophat-1.0.12.ebuild: + Fix x86 compile issue. Thanks to Fabian Groffen. + +*tophat-1.0.12 (07 Dec 2009) + + 07 Dec 2009; Andrey Kislyuk <[email protected]> +metadata.xml, + +tophat-1.0.12.ebuild: + Import from Science overlay and version bump. Thanks to Philippe Veber. + diff --git a/sci-biology/tophat/files/tophat-2.0.9-flags.patch b/sci-biology/tophat/files/tophat-2.0.9-flags.patch new file mode 100644 index 0000000..af89e72 --- /dev/null +++ b/sci-biology/tophat/files/tophat-2.0.9-flags.patch @@ -0,0 +1,109 @@ + configure.ac | 3 ++- + src/Makefile.am | 50 +++++++++++++++++++++++++------------------------- + 2 files changed, 27 insertions(+), 26 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 75e9218..98b05d2 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -68,7 +68,8 @@ AC_CANONICAL_HOST + # set CFLAGS and CXXFLAGS + #user_CFLAGS="${CXXFLAGS}" + user_CFLAGS=${CFLAGS} +-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized" ++#generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized" ++generic_CFLAGS="" + ext_CFLAGS="" + debug_CFLAGS="" + user_LDFLAGS="$LDFLAGS" +diff --git a/src/Makefile.am b/src/Makefile.am +index dde692e..ebb9fcd 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -545,10 +545,10 @@ CLEANFILES = \ + tophat2 + + tophat2: tophat2.in +- sed -e 's|__PREFIX__|$(prefix)|' tophat2.in > tophat2 ++ sed -e 's|__PREFIX__|$(prefix)|' $(top_srcdir)/src/tophat2.in > tophat2 + + tophat: tophat.py +- sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat ++ sed -e 's|__VERSION__|$(VERSION)|' $(top_srcdir)/src/tophat.py > tophat + + #SUFFIXES = .py + #.py: +@@ -617,49 +617,49 @@ libgc_a_SOURCES = \ + #-- program sources + + prep_reads_SOURCES = prep_reads.cpp +-prep_reads_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) +-prep_reads_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++prep_reads_LDADD = libtophat.a $(BAM_LIB) ++prep_reads_LDFLAGS = $(BAM_LDFLAGS) + + segment_juncs_SOURCES = segment_juncs.cpp +-segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) +-segment_juncs_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++segment_juncs_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++segment_juncs_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + + long_spanning_reads_SOURCES = long_spanning_reads.cpp +-long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) +-long_spanning_reads_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++long_spanning_reads_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++long_spanning_reads_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + + gtf_juncs_SOURCES = gtf_juncs.cpp +-gtf_juncs_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) +-gtf_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++gtf_juncs_LDADD = libtophat.a libgc.a $(BAM_LIB) ++gtf_juncs_LDFLAGS = $(BAM_LDFLAGS) + + juncs_db_SOURCES = juncs_db.cpp +-juncs_db_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) +-juncs_db_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++juncs_db_LDADD = libtophat.a $(BAM_LIB) ++juncs_db_LDFLAGS = $(BAM_LDFLAGS) + + tophat_reports_SOURCES = tophat_reports.cpp +-tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) +-tophat_reports_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++tophat_reports_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++tophat_reports_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + + fix_map_ordering_SOURCES = fix_map_ordering.cpp +-fix_map_ordering_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) +-fix_map_ordering_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++fix_map_ordering_LDADD = libtophat.a $(BAM_LIB) ++fix_map_ordering_LDFLAGS = $(BAM_LDFLAGS) + + bam2fastx_SOURCES = bam2fastx.cpp +-bam2fastx_LDADD = $(top_builddir)/src/libgc.a $(BAM_LIB) +-bam2fastx_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++bam2fastx_LDADD = libgc.a $(BAM_LIB) ++bam2fastx_LDFLAGS = $(BAM_LDFLAGS) + + bam_merge_SOURCES = bam_merge.cpp +-bam_merge_LDADD = $(top_builddir)/src/libtophat.a $(top_builddir)/src/libgc.a $(BAM_LIB) +-bam_merge_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++bam_merge_LDADD = libtophat.a libgc.a $(BAM_LIB) ++bam_merge_LDFLAGS = $(BAM_LDFLAGS) + + sam_juncs_SOURCES = sam_juncs.cpp +-sam_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) +-sam_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++sam_juncs_LDADD = libtophat.a $(BAM_LIB) ++sam_juncs_LDFLAGS = $(BAM_LDFLAGS) + + map2gtf_SOURCES = map2gtf.cpp +-map2gtf_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) +-map2gtf_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++map2gtf_LDADD = libtophat.a libgc.a $(BAM_LIB) ++map2gtf_LDFLAGS = $(BAM_LDFLAGS) + + gtf_to_fasta_SOURCES = GTFToFasta.cpp FastaTools.cpp +-gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) +-gtf_to_fasta_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++gtf_to_fasta_LDADD = libtophat.a libgc.a $(BAM_LIB) ++gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS) diff --git a/sci-biology/tophat/metadata.xml b/sci-biology/tophat/metadata.xml new file mode 100644 index 0000000..36cf4a1 --- /dev/null +++ b/sci-biology/tophat/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!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 new file mode 100644 index 0000000..f5f059d --- /dev/null +++ b/sci-biology/tophat/tophat-2.0.12.ebuild @@ -0,0 +1,49 @@ +# 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 +PYTHON_COMPAT=( python2_7 ) + +inherit autotools-utils python-single-r1 + +DESCRIPTION="A fast splice junction mapper for RNA-Seq reads" +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 +SRC_URI="http://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz"; + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug" + +DEPEND="dev-libs/boost" +# sci-biology/seqan provides binaries and headers but there are no *.so files so no need for a runtime dependency +RDEPEND="${DEPEND} + <=sci-biology/bowtie-2.2.3" + +# PATCHES=( "${FILESDIR}"/${P}-flags.patch ) + +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 + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --disable-optim + $(use_enable debug) + ) + autotools-utils_src_configure + sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i Makefile* src/Makefile* || die +} + +src_install() { + 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 new file mode 100644 index 0000000..5e56cc4 --- /dev/null +++ b/sci-biology/tophat/tophat-2.0.13.ebuild @@ -0,0 +1,54 @@ +# 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 +PYTHON_COMPAT=( python2_7 ) + +inherit autotools-utils python-single-r1 + +DESCRIPTION="A fast splice junction mapper for RNA-Seq reads" +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 +SRC_URI="http://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz"; + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug" + +DEPEND="dev-libs/boost" +# >=sci-biology/tophat-2.0.13 contain bundled samtools-0.1.18 and SeqAn-1.3 +# sci-biology/seqan provides binaries and headers but there are no *.so files so no need for a runtime dependency +RDEPEND="${DEPEND} + <=sci-biology/bowtie-2.2.3" + +# PATCHES=( "${FILESDIR}"/${P}-flags.patch ) + +src_prepare() { + sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i configure* Makefile* || die + sed -e "s#./SeqAn-1.3#"${S}"/src/SeqAn-1.3#g" -i configure* || die + # rm -rf src/SeqAn* || die + eautoreconf + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --disable-optim + $(use_enable debug) + ) + autotools-utils_src_configure + cd ../"${P}"_build/src || die + ln -s ../"${P}"/src/SeqAn-1.3 . || die + ln -s ../../"${P}"/src/samtools-0.1.18 . || die + sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i Makefile* || die +} + +src_install() { + autotools-utils_src_install + python_fix_shebang "${ED}"/usr/bin/tophat +} diff --git a/sci-biology/tophat/tophat-2.0.14.ebuild b/sci-biology/tophat/tophat-2.0.14.ebuild new file mode 100644 index 0000000..09b7ce8 --- /dev/null +++ b/sci-biology/tophat/tophat-2.0.14.ebuild @@ -0,0 +1,54 @@ +# 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 +PYTHON_COMPAT=( python2_7 ) + +inherit autotools-utils python-single-r1 + +DESCRIPTION="A fast splice junction mapper for RNA-Seq reads" +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 +SRC_URI="http://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz"; + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug" + +DEPEND="dev-libs/boost" +# >=sci-biology/tophat-2.0.13 contains bundled samtools-0.1.18 and SeqAn-1.3 +# sci-biology/seqan provides binaries and headers but there are no *.so files so no need for a runtime dependency +RDEPEND="${DEPEND} + <=sci-biology/bowtie-2.2.3" +# see https://aur.archlinux.org/packages/tophat/ about linking issues + +# PATCHES=( "${FILESDIR}"/${P}-flags.patch ) + +src_prepare() { + sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i configure* Makefile* || die + sed -e "s#./SeqAn-1.3#"${S}"/src/SeqAn-1.3#g" -i configure* || die + eautoreconf + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --disable-optim + $(use_enable debug) + ) + autotools-utils_src_configure + cd ../"${P}"_build/src || die + ln -s ../../"${P}"/src/SeqAn-1.3 . || die + ln -s ../../"${P}"/src/samtools-0.1.18 . || die + sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i Makefile* || die +} + +src_install() { + autotools-utils_src_install + python_fix_shebang "${ED}"/usr/bin/tophat +}
