diff options
author | Justin Lecher <jlec@gentoo.org> | 2012-07-19 12:03:39 +0000 |
---|---|---|
committer | Justin Lecher <jlec@gentoo.org> | 2012-07-19 12:03:39 +0000 |
commit | 9b760400c9faf29d983e2aba7b8ae300ac5bc350 (patch) | |
tree | b266fe99b1d6a4ec6b9fea680b9b5159936ff4f9 /sci-biology | |
parent | Build with gcc-4.7 Bug #425286 (diff) | |
download | historical-9b760400c9faf29d983e2aba7b8ae300ac5bc350.tar.gz historical-9b760400c9faf29d983e2aba7b8ae300ac5bc350.tar.bz2 historical-9b760400c9faf29d983e2aba7b8ae300ac5bc350.zip |
sci-biology/tophat: Version BUmp; do parallel builds; handle debug build
Package-Manager: portage-2.2.0_alpha120/cvs/Linux x86_64
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/tophat/ChangeLog | 8 | ||||
-rw-r--r-- | sci-biology/tophat/Manifest | 28 | ||||
-rw-r--r-- | sci-biology/tophat/files/tophat-2.0.2-flags.patch | 124 | ||||
-rw-r--r-- | sci-biology/tophat/metadata.xml | 2 | ||||
-rw-r--r-- | sci-biology/tophat/tophat-2.0.0.ebuild | 23 | ||||
-rw-r--r-- | sci-biology/tophat/tophat-2.0.2.ebuild | 31 |
6 files changed, 190 insertions, 26 deletions
diff --git a/sci-biology/tophat/ChangeLog b/sci-biology/tophat/ChangeLog index 93e0142cbc45..f8f1be7bbe04 100644 --- a/sci-biology/tophat/ChangeLog +++ b/sci-biology/tophat/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-biology/tophat # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/ChangeLog,v 1.8 2012/04/25 16:39:53 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/ChangeLog,v 1.9 2012/07/19 12:03:38 jlec Exp $ + +*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: diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest index 21733330fe9b..30504ef117b3 100644 --- a/sci-biology/tophat/Manifest +++ b/sci-biology/tophat/Manifest @@ -1,18 +1,22 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA512 +Hash: SHA256 -DIST tophat-1.0.12.tar.gz 468781 RMD160 b705ca7bde20bd143ba1cfd084b3a3e2815a7a4d SHA1 8a39af78dc9ec797f9f30853fb24b6b0e42d0ef6 SHA256 f67b3f89aa79c7e14b40bcdba87f5aba6d322f869ca4260503e64ffcd2b621b2 -DIST tophat-1.4.1.tar.gz 1420422 RMD160 45073bcf6c46f621595eae58d61a601dd6fe8d93 SHA1 0513bbcadb7194f12fbddeb3e4033e032f2fb29f SHA256 97fd6e09e3cafa90b969dac152585ce5bab4c86f32a980ce2c8ecaac846cd937 -DIST tophat-2.0.0.tar.gz 1750811 RMD160 d72eca16022a67000576034e51138b74fa77654b SHA1 279caa788cd6444d42dcd26091d0c605cd23010a SHA256 1c45812225906fd014ed9671a3696727c6ed0cc5be8f330b3c5ec39a9234be97 -EBUILD tophat-1.0.12.ebuild 948 RMD160 a505db7a21fda8477839ba4f63e81d367c000d84 SHA1 105952f6083033b5ab20aaa75ec5d7cc4f625296 SHA256 c850a45bf9b8463e7eddb461c9da4f84a3628579a56f335e0aeb138c358172b6 -EBUILD tophat-1.4.1.ebuild 703 RMD160 bf5edb3b88a4a87fcf5c5e1fa40f3288427bf3d7 SHA1 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000000000000..ac1ca62da254 --- /dev/null +++ b/sci-biology/tophat/files/tophat-2.0.2-flags.patch @@ -0,0 +1,124 @@ + configure.ac | 6 +++--- + src/Makefile.am | 30 +++++++++++++++--------------- + 2 files changed, 18 insertions(+), 18 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 314a78e..f6933e6 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 -Wuninitialized" ++generic_CFLAGS="" + ext_CFLAGS="" + debug_CFLAGS="" + AC_ARG_ENABLE(intel64, [ --enable-intel64 optimize for Intel64 CPU such as Xeon and Core2], +@@ -84,7 +85,7 @@ AC_ARG_ENABLE([optim], + [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$enable_optim" != xno], [ext_CFLAGS="$ext_CFLAGS -O$enable_optim"]) + AS_IF([test "x$enable_debug" = xyes], + [debug_CFLAGS="-DDEBUG"], + [debug_CFLAGS="-DNDEBUG"]) +@@ -92,7 +93,6 @@ AS_IF([test "x$enable_debug" = xyes], + CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}" + CXXFLAGS="$CFLAGS" + CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS -I./SeqAn-1.3" +-LDFLAGS="$ext_LDFLAGS" + + AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign]) + +diff --git a/src/Makefile.am b/src/Makefile.am +index aa17841..42f9c0c 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -2,7 +2,7 @@ + + #SUBDIRS = samtools + +-#AM_CXXFLAGS = -I$(top_srcdir)/src/SeqAn-1.3 ++AM_CXXFLAGS = -I$(top_srcdir)/src/SeqAn-1.3 + + # Generated with + # find SeqAn-1.3 -type f -print | grep -v ".svn" | sed 's/$/ \\/g' +@@ -550,7 +550,7 @@ CLEANFILES = \ + tophat2 + + tophat2: tophat2.in +- sed -e 's|__PREFIX__|$(prefix)|' tophat2.in > tophat2 ++ sed -e 's|__PREFIX__|$(prefix)|' $(top_srcdir)/src/tophat2.in > tophat2 + + #SUFFIXES = .py + #.py: +@@ -621,53 +621,53 @@ libgc_a_SOURCES = \ + #-- program sources + + prep_reads_SOURCES = prep_reads.cpp +-prep_reads_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) ++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) $(BAM_LIB) ++segment_juncs_LDADD = libtophat.a $(BOOST_THREAD_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) $(BAM_LIB) ++long_spanning_reads_LDADD = libtophat.a $(BOOST_THREAD_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_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_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) $(BAM_LIB) ++tophat_reports_LDADD = libtophat.a $(BOOST_THREAD_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_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_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_LDADD = libtophat.a libgc.a $(BAM_LIB) + bam_merge_LDFLAGS = $(BAM_LDFLAGS) + + closure_juncs_SOURCES = closures.cpp +-closure_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) ++closure_juncs_LDADD = libtophat.a $(BAM_LIB) + closure_juncs_LDFLAGS = $(BAM_LDFLAGS) + + sam_juncs_SOURCES = sam_juncs.cpp +-sam_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) ++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_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_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 index 6631e9455420..8dc2f2067543 100644 --- a/sci-biology/tophat/metadata.xml +++ b/sci-biology/tophat/metadata.xml @@ -7,6 +7,6 @@ </maintainer> <herd>sci-biology</herd> <use> - <flag name='bam'>Compile support for the BAM format</flag> + <flag name="bam">Compile support for the BAM format</flag> </use> </pkgmetadata> diff --git a/sci-biology/tophat/tophat-2.0.0.ebuild b/sci-biology/tophat/tophat-2.0.0.ebuild index b652da021077..de02f86fb3f4 100644 --- a/sci-biology/tophat/tophat-2.0.0.ebuild +++ b/sci-biology/tophat/tophat-2.0.0.ebuild @@ -1,10 +1,12 @@ # Copyright 1999-2012 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/tophat-2.0.0.ebuild,v 1.2 2012/04/25 16:39:53 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/tophat-2.0.0.ebuild,v 1.3 2012/07/19 12:03:38 jlec Exp $ EAPI=4 -inherit flag-o-matic autotools +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils DESCRIPTION="A fast splice junction mapper for RNA-Seq reads" HOMEPAGE="http://tophat.cbcb.umd.edu/" @@ -12,21 +14,18 @@ SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz" LICENSE="Artistic" SLOT="0" -IUSE="+bam" KEYWORDS="~amd64 ~x86" +IUSE="+bam debug" -DEPEND="bam? ( sci-biology/samtools )" +DEPEND=" + dev-libs/boost + bam? ( sci-biology/samtools )" RDEPEND="${DEPEND} sci-biology/bowtie" -MAKEOPTS="${MAKEOPTS} -j1" - -src_prepare() { - filter-ldflags -Wl,--as-needed - eautoreconf -} +PATCHES=( "${FILESDIR}"/${PN}-2.0.2-flags.patch ) src_configure() { - econf \ - $(use_with bam) + local myeconfargs=( $(use_enable debug) ) + autotools-utils_src_configure } diff --git a/sci-biology/tophat/tophat-2.0.2.ebuild b/sci-biology/tophat/tophat-2.0.2.ebuild new file mode 100644 index 000000000000..b84186581aca --- /dev/null +++ b/sci-biology/tophat/tophat-2.0.2.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/tophat-2.0.2.ebuild,v 1.1 2012/07/19 12:03:38 jlec Exp $ + +EAPI=4 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils + +DESCRIPTION="A fast splice junction mapper for RNA-Seq reads" +HOMEPAGE="http://tophat.cbcb.umd.edu/" +SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="+bam debug" + +DEPEND=" + dev-libs/boost + bam? ( sci-biology/samtools )" +RDEPEND="${DEPEND} + sci-biology/bowtie" + +PATCHES=( "${FILESDIR}"/${P}-flags.patch ) + +src_configure() { + local myeconfargs=( $(use_enable debug) ) + autotools-utils_src_configure +} |