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

3 files changed, 184 insertions, 0 deletions

diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest
index 72e63716b604..b269f5d56f90 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 000000000000..c1e8bfd5c5c8
--- /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 000000000000..fc80ea87ea9d
--- /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
+}