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author | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-05-14 20:48:46 +0200 |
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committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-05-14 20:48:46 +0200 |
commit | 4036ac0a6d0616ae423c7de5f5f6dfc60bd83e6f (patch) | |
tree | 5e2fe154531d58cba818446c72442e795348af7e /sci-biology | |
parent | sci-biology/SPAdes: install the package directly using cmake (diff) | |
download | sci-4036ac0a6d0616ae423c7de5f5f6dfc60bd83e6f.tar.gz sci-4036ac0a6d0616ae423c7de5f5f6dfc60bd83e6f.tar.bz2 sci-4036ac0a6d0616ae423c7de5f5f6dfc60bd83e6f.zip |
sci-biology/SPAdes: drop DEPENDency on boost
Upstream says SPAdes uses bundled while modified local copy.
Fix URL to new official site.
Package-Manager: Portage-2.3.5, Repoman-2.3.2
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/SPAdes/SPAdes-3.10.1.ebuild | 14 |
1 files changed, 8 insertions, 6 deletions
diff --git a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild index de93157a4..a887fe909 100644 --- a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild +++ b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild @@ -5,10 +5,10 @@ EAPI=6 PYTHON_COMPAT=( python{2_7,3_{4,5}} ) -inherit eutils toolchain-funcs +inherit eutils toolchain-funcs cmake-utils DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage" -HOMEPAGE="http://bioinf.spbau.ru/en/spades" +HOMEPAGE="http://cab.spbu.ru/software/spades" SRC_URI=" http://spades.bioinf.spbau.ru/release${PV}/SPAdes-${PV}.tar.gz http://spades.bioinf.spbau.ru/release${PV}/manual.html -> ${P}_manual.html @@ -24,10 +24,11 @@ IUSE="" DEPEND=" sys-libs/zlib app-arch/bzip2 - dev-python/regex - dev-libs/boost" + dev-python/regex" RDEPEND="${DEPEND}" - +# BUG: +# SPAdes uses bundled while modified copy of dev-libs/boost +# # BUG: "${S}"/ext/src/ contains plenty of bundled 3rd-party tools. Drop them all and properly DEPEND on their # existing packages # nlopt @@ -44,7 +45,7 @@ RDEPEND="${DEPEND}" # samtools # bwa -# BUG: "${S}"/ext/tools/ contains even two version of bwa +# BUG: "${S}"/ext/tools/ contains even two version of bwa, being installed as bwa-spades binary? # bwa-0.7.12 # bwa-0.6.2 @@ -76,6 +77,7 @@ src_compile(){ src_install(){ cd build_spades || die emake install PREFIX="${ED}"/usr + # cmake-utils_src_install # dies with "${S}" does not appear to contain CMakeLists.txt # BUG: move *.py files to standard site-packages/ subdirectories insinto /usr/share/"${PN}" dodoc "${DISTDIR}"/${P}_*manual.html |