diff options
| -rw-r--r-- | sci-biology/tophat/tophat-2.1.1-r1.ebuild (renamed from sci-biology/tophat/tophat-2.1.1.ebuild) | 18 |
1 files changed, 14 insertions, 4 deletions
diff --git a/sci-biology/tophat/tophat-2.1.1.ebuild b/sci-biology/tophat/tophat-2.1.1-r1.ebuild index fc80ea87ea9d..a8501758f5d9 100644 --- a/sci-biology/tophat/tophat-2.1.1.ebuild +++ b/sci-biology/tophat/tophat-2.1.1-r1.ebuild @@ -6,7 +6,7 @@ EAPI=6 PYTHON_COMPAT=( python2_7 ) -inherit autotools eutils flag-o-matic python-single-r1 +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/" @@ -16,11 +16,14 @@ LICENSE="Artistic" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="debug" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" -RDEPEND="dev-libs/boost +RDEPEND="${PYTHON_DEPS} + dev-libs/boost:= sci-biology/samtools:0.1-legacy sci-biology/bowtie:2" DEPEND="${RDEPEND} + virtual/pkgconfig sci-biology/seqan:1.4" PATCHES=( @@ -46,7 +49,7 @@ src_prepare() { # innocuous non-security flags, prevent log pollution append-cflags -Wno-unused-but-set-variable -Wno-unused-variable - append-cppflags "$(pkg-config --cflags seqan-1.4)" + append-cppflags "$($(tc-getPKG_CONFIG) --cflags seqan-1.4)" eautoreconf } @@ -59,8 +62,15 @@ 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_fix_shebang "${ED}"/usr/bin/${i} + 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 } |