commit: 3bae7944956edffc244eb7d8e55bc0c786013ed0 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sat Apr 9 18:37:04 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat Apr 9 18:57:07 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3bae7944
sci-biology/tophat: Version bump, use samtools:0.1-legacy Gentoo-Bug: 545154, 546816, 566494, 572054 * EAPI=6 * Unbundle samtools and SeqAn * Fix broken shebangs in python scripts Package-Manager: portage-2.2.28 sci-biology/tophat/Manifest | 1 + .../tophat-2.1.1-unbundle-seqan-samtools.patch | 114 +++++++++++++++++++++ sci-biology/tophat/tophat-2.1.1.ebuild | 69 +++++++++++++ 3 files changed, 184 insertions(+) diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest index 72e6371..b269f5d 100644 --- a/sci-biology/tophat/Manifest +++ b/sci-biology/tophat/Manifest @@ -4,3 +4,4 @@ DIST tophat-2.0.0.tar.gz 1750811 SHA256 1c45812225906fd014ed9671a3696727c6ed0cc5 DIST tophat-2.0.2.tar.gz 1759933 SHA256 f9e40ae123dab24d2f2d6896ebf191c8ae3c05c80da6d4d965defe7579d553e0 SHA512 8341d406bfc2b86323932a151ad60469c6d50031bace433c5e3b6678a92eaed3516744fb9077d0e8944018275642050e2e9aca0126b4dd69423754c3dc9ae83c WHIRLPOOL 45a52fc96b258f4ae0b5b7a4d1dc4c22885e0b9230891dde1db85671deeceb3213008de02878cc3b1f9dc6af68b40bc897f691a1835bd4abf29d1a2bde42e1c2 DIST tophat-2.0.8.tar.gz 1757036 SHA256 07d323d295effc99d4e261439c5ba2e10d5530af078e5de97c1a7bf1cbdd0da1 SHA512 c69360cc2f558c37d14b6a0e006f2483771ce5cdb42dc8397dd15a944a61d762843158adbf7c2bc89c2d4db46d9a02633dbd2721bf3376ef5d3ae6fb153db100 WHIRLPOOL a97ad6d47be23089605578a6f8ff9434afcb27a9fa58118b5b923af1d79530614af9fcaf5ebda2043603bf2dd8b10c2b7636e7b14662b9ab4f6e2059da4cb2b2 DIST tophat-2.0.9.tar.gz 1766681 SHA256 9b506bbfdbb14b296d804557a50f41cc167480dfeed66a31c33e2ffb580afd38 SHA512 a81b801ee6c1f643d1fa507c2372d43ccdf4922d3f7ab76a34442c96aee78a3afc4a47ba164d46c6b6b6451aeae78b711c44c118e584da742940f74af7bc9610 WHIRLPOOL a67392251e592df62deb3fe58dcc4eadd0d0b1fe0a09389e48f1f30a7c591343794d1e1b2a27467c0a0f5a0e84dd5a5fbdef538a5bcf1b80ba8972e6ec02fbcf +DIST tophat-2.1.1.tar.gz 2259554 SHA256 37840b96f3219630082b15642c47f5ef95d14f6ee99c06a369b08b3d05684da5 SHA512 e2e0943a6f3d34b83922e6e403b65a3bee480a2b2bb4bf2de0cae7e0ef5bb166b66fec923316c2b643e8550e43c842f0f1bcc2ca7249d20fbcf5a4733fbdeabc WHIRLPOOL 1e0d2bc4031eaa56a3b77ca5966c2ed439a85c9b05f028f69f4477d517e51371156bbe73d499536148eb42d60641af7f294641ee79bc855fcc4df74d70dae26c 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 new file mode 100644 index 0000000..c1e8bfd --- /dev/null +++ b/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch @@ -0,0 +1,114 @@ +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 @@ + fi + + +-# BAM related: +- ac_bam_path=samtools-0.1.18 +- BAM_LIB="-lbam" +- BAM_LDFLAGS="-L./$ac_bam_path" +- BAM_CPPFLAGS="-I./$ac_bam_path" +- AC_SUBST(BAM_CPPFLAGS) +- AC_SUBST(BAM_LDFLAGS) +- AC_SUBST(BAM_LIB) +- +- + # Checks for header files. + AC_CHECK_HEADERS([stdlib.h string.h unistd.h]) + +@@ -80,32 +70,23 @@ + # set CFLAGS and CXXFLAGS + #user_CFLAGS="${CXXFLAGS}" + user_CFLAGS=${CFLAGS} +-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized" ++generic_CFLAGS="" + ext_CFLAGS="" + debug_CFLAGS="" + user_LDFLAGS="$LDFLAGS" + +-AC_ARG_ENABLE(intel64, [ --enable-intel64 optimize for Intel64 CPU such as Xeon and Core2], +- [ext_CFLAGS="${ext_CFLAGS} -mtune=nocona"], []) +- + AC_ARG_ENABLE([debug], + [AS_HELP_STRING([--enable-debug], + [enable debugging info (default is no)])], + [], [enable_debug=no]) +-AC_ARG_ENABLE([optim], +- [AS_HELP_STRING([--enable-optim@<:@=0|1|2|3@:>@], +- [set optimization level (default is 3)])], +- [if test "x$enable_optim" = xyes; then enable_optim=3; fi], +- [enable_optim=3]) + +-AS_IF([test "x$enable_optim" != xno], [ext_CFLAGS="$ext_CFLAGS -O$enable_optim"]) + AS_IF([test "x$enable_debug" = xyes], + [debug_CFLAGS="-DDEBUG"], + [debug_CFLAGS="-DNDEBUG"]) + + CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}" + CXXFLAGS="$CFLAGS" +-CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS -I./SeqAn-1.4.2" ++CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS" + LDFLAGS="$BAM_LDFLAGS $BOOST_LDFLAGS $user_LDFLAGS" + + AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign]) +--- tophat-2.1.1/src/Makefile.am ++++ tophat-2.1.1/src/Makefile.am +@@ -683,17 +683,12 @@ + SeqAn-1.4.2/seqan/system/system_thread.h \ + SeqAn-1.4.2/seqan/version.h + +-SAMDIR = ./samtools-0.1.18 +-SAMLIB = libbam.a +-SAMPROG = samtools_0.1.18 +-BAM_LIB = -lbam +-BAM_CPPFLAGS = -I$(SAMDIR) +-BAM_LDFLAGS = -L$(SAMDIR) ++BAM_LIB = -lbam-0.1-legacy ++AM_CPPFLAGS = -I/usr/include/bam-0.1-legacy/ + + #-- progs to be installed in $prefix/bin + + bin_PROGRAMS = \ +- $(SAMPROG) \ + prep_reads \ + gtf_to_fasta \ + fix_map_ordering \ +@@ -722,9 +717,6 @@ + tophat2 \ + tophat + +-clean-local: +- cd $(SAMDIR) && make clean +- + tophat2: tophat2.sh + cp tophat2.sh tophat2 && chmod 755 tophat2 + +@@ -732,7 +724,7 @@ + sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat && chmod 755 tophat + + #-- tophat library for linking convienence +-noinst_LIBRARIES = $(SAMLIB) libgc.a libtophat.a ++noinst_LIBRARIES = libgc.a libtophat.a + + noinst_HEADERS = \ + reads.h \ +@@ -844,15 +836,5 @@ + gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) + gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) + +- +-libbam_a_SOURCES = +-samtools_0_1_18_SOURCES = +- +-$(SAMPROG): $(SAMLIB) +- +- +-$(SAMLIB): +- cd $(SAMDIR) && make $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) .. +- + install-data-hook: + cp -r intervaltree sortedcontainers $(DESTDIR)$(bindir) diff --git a/sci-biology/tophat/tophat-2.1.1.ebuild b/sci-biology/tophat/tophat-2.1.1.ebuild new file mode 100644 index 0000000..fc80ea8 --- /dev/null +++ b/sci-biology/tophat/tophat-2.1.1.ebuild @@ -0,0 +1,69 @@ +# 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 + +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/${P}.tar.gz"; + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug" + +RDEPEND="dev-libs/boost + sci-biology/samtools:0.1-legacy + sci-biology/bowtie:2" +DEPEND="${RDEPEND} + sci-biology/seqan:1.4" + +PATCHES=( + "${FILESDIR}/${P}-unbundle-seqan-samtools.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 "$(pkg-config --cflags seqan-1.4)" + + eautoreconf +} + +src_configure() { + econf $(use_enable debug) +} + +src_install() { + default + + local i + for i in bed_to_juncs contig_to_chr_coords sra_to_solid tophat tophat-fusion-post; do + python_fix_shebang "${ED}"/usr/bin/${i} + done +} + +pkg_postinst() { + optfeature "ABI SOLiD colorspace reads" sci-biology/bowtie:1 +}
