* [gentoo-commits] proj/sci:master commit in: sci-biology/tophat/files/, sci-biology/tophat/
@ 2015-04-27 11:09 Martin Mokrejs
0 siblings, 0 replies; 2+ messages in thread
From: Martin Mokrejs @ 2015-04-27 11:09 UTC (permalink / raw
To: gentoo-commits
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@gentoo.org> 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@gentoo.org> +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@gentoo.org> +tophat-2.0.8.ebuild,
+ +files/tophat-2.0.8-flags.patch:
+ Version Bump; unbundle sci-biology/seqan
+
+ 12 Mar 2013; Justin Lecher <jlec@gentoo.org> 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@gentoo.org> 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@gentoo.org> 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@gentoo.org> -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@gentoo.org> -tophat-1.3.2.ebuild,
+ +tophat-1.3.3.ebuild, +tophat-1.4.1.ebuild:
+ version bump
+
+ 04 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> tophat-1.3.2.ebuild:
+ filter as-needed
+
+*tophat-1.3.2 (26 Sep 2011)
+
+ 26 Sep 2011; Andrey Kislyuk <weaver@gentoo.org> +tophat-1.3.2.ebuild:
+ Version bump
+
+ 05 Apr 2010; Pawel Hajdan jr <phajdan.jr@gentoo.org> tophat-1.0.12.ebuild:
+ x86 stable wrt bug #311829
+
+ 29 Mar 2010; Pacho Ramos <pacho@gentoo.org> tophat-1.0.12.ebuild:
+ amd64 stable, bug 311829
+
+ 07 Dec 2009; Andrey Kislyuk <weaver@gentoo.org> 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@gentoo.org> +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
+}
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/tophat/files/, sci-biology/tophat/
@ 2016-04-13 10:47 Marius Brehler
0 siblings, 0 replies; 2+ messages in thread
From: Marius Brehler @ 2016-04-13 10:47 UTC (permalink / raw
To: gentoo-commits
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>sci-biology@gentoo.org</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
-}
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2016-04-13 10:47 [gentoo-commits] proj/sci:master commit in: sci-biology/tophat/files/, sci-biology/tophat/ Marius Brehler
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