From 95f436ca3a6e4e65e9db762b7d0da99172593042 Mon Sep 17 00:00:00 2001 From: David Seifert Date: Sun, 25 Sep 2016 14:26:00 +0200 Subject: sci-biology/tophat: USE="threads" dep on dev-libs/boost Gentoo-bug: 594810 * Remove autoconf macros from archive, depend on sys-devel/autoconf instead for the latest versions. Package-Manager: portage-2.3.1 --- .../tophat-2.1.1-unbundle-seqan-samtools.patch | 60 +++++++++++++-- sci-biology/tophat/tophat-2.1.1-r1.ebuild | 80 -------------------- sci-biology/tophat/tophat-2.1.1-r2.ebuild | 85 ++++++++++++++++++++++ 3 files changed, 139 insertions(+), 86 deletions(-) delete mode 100644 sci-biology/tophat/tophat-2.1.1-r1.ebuild create mode 100644 sci-biology/tophat/tophat-2.1.1-r2.ebuild (limited to 'sci-biology') diff --git a/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch b/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch index c1e8bfd5c5c8..9d0a2694051a 100644 --- a/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch +++ b/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch @@ -1,9 +1,25 @@ Unbundle the included samtools and SeqAn, and use system libraries. See also: https://bugs.gentoo.org/show_bug.cgi?id=566494 ---- tophat-2.1.1/configure.ac -+++ tophat-2.1.1/configure.ac -@@ -38,16 +38,6 @@ +Remove ancient ax_boost_base.m4 and ax_boost_thread.m4, and depend +on >=sys-devel/autoconf-archive-2016.09.16 in the ebuild instead. +See also: https://bugs.gentoo.org/show_bug.cgi?id=594810 + +--- a/configure.ac ++++ b/configure.ac +@@ -28,26 +28,15 @@ + AC_PROG_INSTALL + AM_PATH_PYTHON([2.4]) + +-m4_include([ax_boost_base.m4]) +-m4_include([ax_boost_thread.m4]) + # CXXFLAGS="$CXXFLAGS $threadLib" + AX_BOOST_BASE([1.38.0]) ++AX_BOOST_SYSTEM + AX_BOOST_THREAD +-if test -z "$BOOST_THREAD_LIBS"; then ++if test -z "$BOOST_THREAD_LIB"; then + AC_MSG_ERROR([boost.thread not found. Aborting.]) fi @@ -20,7 +36,7 @@ See also: https://bugs.gentoo.org/show_bug.cgi?id=566494 # Checks for header files. AC_CHECK_HEADERS([stdlib.h string.h unistd.h]) -@@ -80,32 +70,23 @@ +@@ -80,32 +69,23 @@ # set CFLAGS and CXXFLAGS #user_CFLAGS="${CXXFLAGS}" user_CFLAGS=${CFLAGS} @@ -55,8 +71,17 @@ See also: https://bugs.gentoo.org/show_bug.cgi?id=566494 LDFLAGS="$BAM_LDFLAGS $BOOST_LDFLAGS $user_LDFLAGS" AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign]) ---- tophat-2.1.1/src/Makefile.am -+++ tophat-2.1.1/src/Makefile.am +@@ -122,7 +102,7 @@ + -- ${PACKAGE_STRING} Configuration Results -- + C++ compiler: ${CXX} ${CXXFLAGS} + Linker flags: ${LDFLAGS} +- BOOST libraries: ${BOOST_THREAD_LIBS}" ++ BOOST libraries: ${BOOST_THREAD_LIB}" + + if test x"${GCC}" = x"yes" ; then + gcc_version=`${CC} --version | head -n 1` +--- a/src/Makefile.am ++++ b/src/Makefile.am @@ -683,17 +683,12 @@ SeqAn-1.4.2/seqan/system/system_thread.h \ SeqAn-1.4.2/seqan/version.h @@ -96,6 +121,29 @@ See also: https://bugs.gentoo.org/show_bug.cgi?id=566494 noinst_HEADERS = \ reads.h \ +@@ -801,11 +793,11 @@ + prep_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) + + segment_juncs_SOURCES = segment_juncs.cpp +-segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) + segment_juncs_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS) + + long_spanning_reads_SOURCES = long_spanning_reads.cpp +-long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) + long_spanning_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS) + + gtf_juncs_SOURCES = gtf_juncs.cpp +@@ -817,7 +809,7 @@ + juncs_db_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) + + tophat_reports_SOURCES = tophat_reports.cpp +-tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) + tophat_reports_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS) + + fix_map_ordering_SOURCES = fix_map_ordering.cpp @@ -844,15 +836,5 @@ gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) diff --git a/sci-biology/tophat/tophat-2.1.1-r1.ebuild b/sci-biology/tophat/tophat-2.1.1-r1.ebuild deleted file mode 100644 index 6c6690a7a86e..000000000000 --- a/sci-biology/tophat/tophat-2.1.1-r1.ebuild +++ /dev/null @@ -1,80 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools eutils flag-o-matic python-single-r1 toolchain-funcs - -DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie2" -HOMEPAGE="https://ccb.jhu.edu/software/tophat/" -SRC_URI="https://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="debug" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - dev-libs/boost:= - sci-biology/samtools:0.1-legacy - sci-biology/bowtie:2" -DEPEND="${RDEPEND} - virtual/pkgconfig - sci-biology/seqan:1.4" - -PATCHES=( - "${FILESDIR}/${P}-unbundle-seqan-samtools.patch" - "${FILESDIR}/${P}-fix-c++14.patch" -) - -src_prepare() { - default - - # remove bundled libs - rm -rf src/samtools-0.1.18/ src/SeqAn-1.4.2/ || die - - sed -e "s:samtools_0.1.18:${EPREFIX}/usr/bin/samtools-0.1-legacy/samtools:" \ - -i src/tophat.py src/common.cpp || die - - sed -e "s:/usr/include/bam-0.1-legacy/:${EPREFIX}/usr/include/bam-0.1-legacy/:" \ - -e '/^samtools-0\.1\.18\//d' \ - -e '/^SeqAn-1\.4\.2\//d' \ - -e 's:sortedcontainers/sortedset.py \\:sortedcontainers/sortedset.py:' \ - -e 's:\$(top_builddir)\/src\/::' \ - -i src/Makefile.am || die - sed -e 's:\$(top_builddir)\/src\/::' -i src/Makefile.am || die - - # innocuous non-security flags, prevent log pollution - append-cflags -Wno-unused-but-set-variable -Wno-unused-variable - append-cppflags "$($(tc-getPKG_CONFIG) --cflags seqan-1.4)" - - eautoreconf -} - -src_configure() { - econf $(use_enable debug) -} - -src_install() { - default - - local i - # install scripts properly - for i in bed_to_juncs contig_to_chr_coords sra_to_solid tophat tophat-fusion-post; do - python_doscript "${ED%/}/usr/bin/${i}" - done - - # install python modules properly - for i in intervaltree sortedcontainers; do - python_domodule "${ED%/}/usr/bin/${i}" - rm -rf "${ED%/}/usr/bin/${i}" || die - done -} - -pkg_postinst() { - optfeature "ABI SOLiD colorspace reads" sci-biology/bowtie:1 -} diff --git a/sci-biology/tophat/tophat-2.1.1-r2.ebuild b/sci-biology/tophat/tophat-2.1.1-r2.ebuild new file mode 100644 index 000000000000..52a75a6d5964 --- /dev/null +++ b/sci-biology/tophat/tophat-2.1.1-r2.ebuild @@ -0,0 +1,85 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit autotools eutils flag-o-matic python-single-r1 toolchain-funcs + +DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie2" +HOMEPAGE="https://ccb.jhu.edu/software/tophat/" +SRC_URI="https://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + dev-libs/boost:=[threads] + sci-biology/samtools:0.1-legacy + sci-biology/bowtie:2" +DEPEND="${RDEPEND} + virtual/pkgconfig + sci-biology/seqan:1.4 + >=sys-devel/autoconf-archive-2016.09.16" + +PATCHES=( + "${FILESDIR}/${P}-unbundle-seqan-samtools.patch" + "${FILESDIR}/${P}-fix-c++14.patch" +) + +src_prepare() { + default + + # remove bundled libs + rm -rf src/samtools-0.1.18/ src/SeqAn-1.4.2/ || die + + sed -e "s:samtools_0.1.18:${EPREFIX}/usr/bin/samtools-0.1-legacy/samtools:" \ + -i src/tophat.py src/common.cpp || die + + sed -e "s:/usr/include/bam-0.1-legacy/:${EPREFIX}/usr/include/bam-0.1-legacy/:" \ + -e '/^samtools-0\.1\.18\//d' \ + -e '/^SeqAn-1\.4\.2\//d' \ + -e 's:sortedcontainers/sortedset.py \\:sortedcontainers/sortedset.py:' \ + -e 's:\$(top_builddir)\/src\/::' \ + -i src/Makefile.am || die + sed -e 's:\$(top_builddir)\/src\/::' -i src/Makefile.am || die + + # innocuous non-security flags, prevent log pollution + append-cflags -Wno-unused-but-set-variable -Wno-unused-variable + append-cppflags "$($(tc-getPKG_CONFIG) --cflags seqan-1.4)" + + # remove ancient autoconf archive macros, wreaking havoc, + # depend on sys-devel/autoconf-archive instead, bug #594810 + rm {ax_boost_thread,ax_boost_base}.m4 || die + + eautoreconf +} + +src_configure() { + econf $(use_enable debug) +} + +src_install() { + default + + local i + # install scripts properly + for i in bed_to_juncs contig_to_chr_coords sra_to_solid tophat tophat-fusion-post; do + python_doscript "${ED%/}/usr/bin/${i}" + done + + # install python modules properly + for i in intervaltree sortedcontainers; do + python_domodule "${ED%/}/usr/bin/${i}" + rm -rf "${ED%/}/usr/bin/${i}" || die + done +} + +pkg_postinst() { + optfeature "ABI SOLiD colorspace reads" sci-biology/bowtie:1 +} -- cgit v1.2.3-65-gdbad