commit: f9e1e46a3cfd7b433da489e1e4da8b1445755a13
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Apr 9 19:16:41 2016 +0000
Commit: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Sat Apr 9 19:16:41 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f9e1e46a
sci-biology/tophat: remove all ebuilds, latest version in main tree
sci-biology/tophat/files/tophat-2.0.9-flags.patch | 109 ----------------------
sci-biology/tophat/metadata.xml | 11 ---
sci-biology/tophat/tophat-2.0.12.ebuild | 58 ------------
sci-biology/tophat/tophat-2.0.13.ebuild | 61 ------------
sci-biology/tophat/tophat-2.0.14.ebuild | 62 ------------
sci-biology/tophat/tophat-2.1.0.ebuild | 43 ---------
6 files changed, 344 deletions(-)
diff --git a/sci-biology/tophat/files/tophat-2.0.9-flags.patch
b/sci-biology/tophat/files/tophat-2.0.9-flags.patch
deleted file mode 100644
index af89e72..0000000
--- a/sci-biology/tophat/files/tophat-2.0.9-flags.patch
+++ /dev/null
@@ -1,109 +0,0 @@
- 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
deleted file mode 100644
index dce054e..0000000
--- a/sci-biology/tophat/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
-<pkgmetadata>
- <maintainer type="project">
- <email>[email protected]</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">infphilo/tophat</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/tophat/tophat-2.0.12.ebuild
b/sci-biology/tophat/tophat-2.0.12.ebuild
deleted file mode 100644
index 7c9cf07..0000000
--- a/sci-biology/tophat/tophat-2.0.12.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=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";
-# 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/${P}.tar.gz";
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug"
-
-DEPEND="dev-libs/boost"
-# sci-biology/seqan provides binaries and headers but there are no *.so files
so no need for a runtime dependency
-# boost and seqan is needed for tophat_reporter
-
-# tophat.py calls
-# samtools_0.1.18 view -h -
-# samtools_0.1.18 sort
-# samtools_0.1.18 merge -f -h -u -Q --sam-header
-RDEPEND="${DEPEND}
- >=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5
<=sci-biology/bowtie-2.2.3 )"
-
-# 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
- eautoreconf
- 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() {
- # 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
deleted file mode 100644
index 6625162..0000000
--- a/sci-biology/tophat/tophat-2.0.13.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=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";
-# 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/${P}.tar.gz";
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug"
-
-DEPEND="dev-libs/boost"
-# sci-biology/seqan provides binaries and headers but there are no *.so files
so no need for a runtime dependency
-# boost and seqan is needed for tophat_reporter
-
-# tophat.py calls
-# samtools_0.1.18 view -h -
-# samtools_0.1.18 sort
-# samtools_0.1.18 merge -f -h -u -Q --sam-header
-RDEPEND="${DEPEND}
- >=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5
<=sci-biology/bowtie-2.2.3 )"
-
-# 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#"${S}"/src/samtools-0.1.18#g" -i Makefile*
|| die
-}
-
-src_install() {
- # introduce empty all-recursive: target in
tophat-2.0.14_build/src/Makefile (BUG: does not replace?)
- sed -e "s#^all: all-am#all: all-am\nall-recursive: all#g" -i
src/Makefile* || die
- autotools-utils_src_install
- python_fix_shebang "${ED}"/usr/bin/tophat
-}
diff --git a/sci-biology/tophat/tophat-2.0.14.ebuild
b/sci-biology/tophat/tophat-2.0.14.ebuild
deleted file mode 100644
index 0b8f1e8..0000000
--- a/sci-biology/tophat/tophat-2.0.14.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=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";
-# 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/${P}.tar.gz";
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug"
-
-DEPEND="dev-libs/boost"
-# sci-biology/seqan provides binaries and headers but there are no *.so files
so no need for a runtime dependency
-# boost and seqan is needed for tophat_reporter
-
-# tophat.py calls
-# samtools_0.1.18 view -h -
-# samtools_0.1.18 sort
-# samtools_0.1.18 merge -f -h -u -Q --sam-header
-RDEPEND="${DEPEND}
- >=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5
<=sci-biology/bowtie-2.2.3 )"
-
-# 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#"${S}"/src/samtools-0.1.18#g" -i Makefile*
|| die
-}
-
-src_install() {
- # introduce empty all-recursive: target in
tophat-2.0.14_build/src/Makefile (BUG: does not replace?)
- sed -e "s#^all: all-am#all: all-am\nall-recursive: all#g" -i
src/Makefile* || die
- autotools-utils_src_install
- python_fix_shebang "${ED}"/usr/bin/tophat
-}
diff --git a/sci-biology/tophat/tophat-2.1.0.ebuild
b/sci-biology/tophat/tophat-2.1.0.ebuild
deleted file mode 100644
index 05a7bfa..0000000
--- a/sci-biology/tophat/tophat-2.1.0.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-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
-}
