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

[Martin Mokrejs]

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 <pinkbyte@g.o> 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 <jlec@g.o> +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 <jlec@g.o> +tophat-2.0.8.ebuild,
+  +files/tophat-2.0.8-flags.patch:
+  Version Bump; unbundle sci-biology/seqan
+
+  12 Mar 2013; Justin Lecher <jlec@g.o> 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 <jlec@g.o> 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 <jlec@g.o> 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 <weaver@g.o> -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 <weaver@g.o> -tophat-1.3.2.ebuild,
+  +tophat-1.3.3.ebuild, +tophat-1.4.1.ebuild:
+  version bump
+
+  04 Feb 2012; Andrey Kislyuk <weaver@g.o> tophat-1.3.2.ebuild:
+  filter as-needed
+
+*tophat-1.3.2 (26 Sep 2011)
+
+  26 Sep 2011; Andrey Kislyuk <weaver@g.o> +tophat-1.3.2.ebuild:
+  Version bump
+
+  05 Apr 2010; Pawel Hajdan jr <phajdan.jr@g.o> tophat-1.0.12.ebuild:
+  x86 stable wrt bug #311829
+
+  29 Mar 2010; Pacho Ramos <pacho@g.o> tophat-1.0.12.ebuild:
+  amd64 stable, bug 311829
+
+  07 Dec 2009; Andrey Kislyuk <weaver@g.o> 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 <weaver@g.o> +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
+}