--- /dev/null
+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)
--- /dev/null
+# 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
+}
projects / gentoo.git / commitdiff