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

1 files changed, 85 insertions, 0 deletions

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
+}