sci-biology/tophat: Various QA fixes, handle python properly

* Add subslot operator := for dev-libs/boost
* DEPEND on virtual/pkgconfig
* Add missing ${PYTHON_REQUIRED_USE} and ${PYTHON_DEPS}
* Install python scripts and modules properly using
  'python_doscript' and 'python_domodule'

Package-Manager: portage-2.3.0

diff --git a/sci-biology/tophat/tophat-2.1.1.ebuild b/sci-biology/tophat/tophat-2.1.1-r1.ebuild
similarity index 76%
rename from sci-biology/tophat/tophat-2.1.1.ebuild
rename to sci-biology/tophat/tophat-2.1.1-r1.ebuild
index fc80ea87ea9da87b03f292b119945d0a0495039b..a8501758f5d91a9cbedc3107b7633a6566df34e8 100644 (file)
--- 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
 }