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commit: 1fef751f90def6048c9066f9c5cc35bcc6681a33 |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Sat Sep 3 08:37:31 2016 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Sat Sep 3 08:37:51 2016 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1fef751f |
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|
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sci-biology/tophat: Various QA fixes, handle python properly |
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|
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* Add subslot operator := for dev-libs/boost |
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* DEPEND on virtual/pkgconfig |
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* Add missing ${PYTHON_REQUIRED_USE} and ${PYTHON_DEPS} |
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* Install python scripts and modules properly using |
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'python_doscript' and 'python_domodule' |
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|
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Package-Manager: portage-2.3.0 |
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|
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.../{tophat-2.1.1.ebuild => tophat-2.1.1-r1.ebuild} | 18 ++++++++++++++---- |
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1 file changed, 14 insertions(+), 4 deletions(-) |
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|
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diff --git a/sci-biology/tophat/tophat-2.1.1.ebuild b/sci-biology/tophat/tophat-2.1.1-r1.ebuild |
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similarity index 76% |
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rename from sci-biology/tophat/tophat-2.1.1.ebuild |
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rename to sci-biology/tophat/tophat-2.1.1-r1.ebuild |
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index fc80ea8..a850175 100644 |
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--- a/sci-biology/tophat/tophat-2.1.1.ebuild |
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+++ b/sci-biology/tophat/tophat-2.1.1-r1.ebuild |
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@@ -6,7 +6,7 @@ EAPI=6 |
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|
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PYTHON_COMPAT=( python2_7 ) |
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|
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-inherit autotools eutils flag-o-matic python-single-r1 |
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+inherit autotools eutils flag-o-matic python-single-r1 toolchain-funcs |
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|
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DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie2" |
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HOMEPAGE="https://ccb.jhu.edu/software/tophat/" |
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@@ -16,11 +16,14 @@ LICENSE="Artistic" |
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SLOT="0" |
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KEYWORDS="~amd64 ~x86" |
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IUSE="debug" |
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+REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
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|
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-RDEPEND="dev-libs/boost |
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+RDEPEND="${PYTHON_DEPS} |
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+ dev-libs/boost:= |
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sci-biology/samtools:0.1-legacy |
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sci-biology/bowtie:2" |
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DEPEND="${RDEPEND} |
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+ virtual/pkgconfig |
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sci-biology/seqan:1.4" |
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|
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PATCHES=( |
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@@ -46,7 +49,7 @@ src_prepare() { |
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|
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# innocuous non-security flags, prevent log pollution |
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append-cflags -Wno-unused-but-set-variable -Wno-unused-variable |
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- append-cppflags "$(pkg-config --cflags seqan-1.4)" |
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+ append-cppflags "$($(tc-getPKG_CONFIG) --cflags seqan-1.4)" |
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|
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eautoreconf |
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} |
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@@ -59,8 +62,15 @@ src_install() { |
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default |
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|
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local i |
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+ # install scripts properly |
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for i in bed_to_juncs contig_to_chr_coords sra_to_solid tophat tophat-fusion-post; do |
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- python_fix_shebang "${ED}"/usr/bin/${i} |
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+ python_doscript "${ED%/}/usr/bin/${i}" |
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+ done |
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+ |
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+ # install python modules properly |
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+ for i in intervaltree sortedcontainers; do |
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+ python_domodule "${ED%/}/usr/bin/${i}" |
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+ rm -rf "${ED%/}/usr/bin/${i}" || die |
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done |
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} |