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| author |   Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2018-01-09 23:03:02 +0100 |
|---|---|---|
| committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2018-01-09 23:03:02 +0100 |
| commit | 4dd7fc5f1806465684c1101c88021ab3e1993fa2 (patch) | |
| tree | 4bcae8f623062e733cf3def2badbef953978b8eb | |
| parent | sci-biology/BRAKER: version bump (diff) | |
| download | sci-4dd7fc5f1806465684c1101c88021ab3e1993fa2.tar.gz sci-4dd7fc5f1806465684c1101c88021ab3e1993fa2.tar.bz2 sci-4dd7fc5f1806465684c1101c88021ab3e1993fa2.zip | |
sci-biology/SPAdes: version bump
Try to follow the upstream's approach to compile and install
the tool. src_compile() therefore does also src_install()
into a DESTDIR.
Package-Manager: Portage-2.3.19, Repoman-2.3.6
| -rw-r--r-- | sci-biology/SPAdes/Manifest | 5 | ||||
| -rw-r--r-- | sci-biology/SPAdes/SPAdes-3.11.1.ebuild | 72 |
2 files changed, 77 insertions, 0 deletions
diff --git a/sci-biology/SPAdes/Manifest b/sci-biology/SPAdes/Manifest index 1e14b8e68..f7c0aab30 100644 --- a/sci-biology/SPAdes/Manifest +++ b/sci-biology/SPAdes/Manifest @@ -3,3 +3,8 @@ DIST SPAdes-3.10.1_dipspades_manual.html 12561 BLAKE2B adacd4a195a1ae4ce400907d7 DIST SPAdes-3.10.1_manual.html 60105 BLAKE2B beb76d87cc72edf5edf61a915b3e27b0c89d2a71ffd9c7dce757f08cf42b895fb815ad442d0700aab57ec60ed097cdf33ff629f43ccb1a1cb44f0e4d9c7cc311 SHA512 ce69945b00eee73a4384b284fcd66e3d9f0619cf9c3eb76311604ba749841fe5b56208fcd2fdd02455567ad3c0125312dc80f67d69137c66f8805c709f39041c DIST SPAdes-3.10.1_rnaspades_manual.html 4676 BLAKE2B fa39bd4be56ea07d4231b95516718532d1d5ef3cb4e49f91b63a06552e15798d814e402d1d73ab73295ff0e8b86bb786be9ead2689d1fb0dd4f185ce9dec3648 SHA512 68d5dc92c6bc7c865221d52a45d056657cf80ecb4a3d25f49b68ad6e654d353372e9ce862dbf9c164da310a703a31e81f5af68b8ceab1d64651134650fce4cff DIST SPAdes-3.10.1_truspades_manual.html 10769 BLAKE2B ec2788a9dfdb783b8e922517263d54177595c4c6b6feee7d4c6122c3c7db561a8e2f31d210af1d6384aeb9554fb551a3ddb9937bcaf185ad6707d8c3f049f48a SHA512 e19a9385ae63f32cb232c90abd16eb8563b6b8f0abcdb2aadcfdf35cfe4aee8cf329fc97e5a2a7149ac9c6fce40791b5a89c9431de90d6e1d3651b6f0a5e221b +DIST SPAdes-3.11.1.tar.gz 8720396 BLAKE2B d5cc786958c6006bd41fd3c3872dc5c980961459d832b6cc00f1b39de981860272a1c8b156fa307dda3afb8a16ef500eb2bf891791373e7a5e637baeb2e2b6a8 SHA512 fc6627d7a2d139fb8123278648afdd517fe993e60bb12fcf16764fc8db9f8d347796bc31365f602050448d320c90119363f4a128fb9a52478d3df488f0e73ad9 +DIST SPAdes-3.11.1_dipspades_manual.html 12561 BLAKE2B adacd4a195a1ae4ce400907d728aa9df9398ffd8545777dc2d5a69cab4396e73825e4e8f42d3d590cf82ec4f6cbb0e4783d3d731b6637b0ce8cf8afe2ebe689b SHA512 618284c899b5c0f167b91638ac3ca4d7ee2c932f5acbfa6225f43276b073259000022f12afa3d8df26dfd967085b3d2d11ca006766169199afc02de111a78db4 +DIST SPAdes-3.11.1_manual.html 60400 BLAKE2B 9ce91d0192e7e77e70f9f787f892ac951508f3fe3be4c72206fe51789e983fd229e28cf28711173a9cbb95fa3dec384422c4dfb98f3fd48b2a2cc33e90ed4e21 SHA512 d88857cd75278d051da6f2d936fa70c4c2c862e1c1598cd83d7276823fd822ff6defe4b06214b28938de9e1bc6e63a0fb70c7196c76291c85d491740ffce0e8f +DIST SPAdes-3.11.1_rnaspades_manual.html 6408 BLAKE2B 90cd5b7f5624a9edfb8d584288aa4c2d4d71fa8f704308e33549776931647c0c1ed640bb21159f036255e7fa43c8f77292b4396bd6858758f871859eceaab13a SHA512 39acd4ce301708b67201d04c9ae3f994c196914a849e030f736b318aa3b38af3a50a452e467e7496c8a5402d69d17ceffd245e2bde6eb2bb769dc8e780c9e442 +DIST SPAdes-3.11.1_truspades_manual.html 10769 BLAKE2B ec2788a9dfdb783b8e922517263d54177595c4c6b6feee7d4c6122c3c7db561a8e2f31d210af1d6384aeb9554fb551a3ddb9937bcaf185ad6707d8c3f049f48a SHA512 e19a9385ae63f32cb232c90abd16eb8563b6b8f0abcdb2aadcfdf35cfe4aee8cf329fc97e5a2a7149ac9c6fce40791b5a89c9431de90d6e1d3651b6f0a5e221b diff --git a/sci-biology/SPAdes/SPAdes-3.11.1.ebuild b/sci-biology/SPAdes/SPAdes-3.11.1.ebuild new file mode 100644 index 000000000..1842fca37 --- /dev/null +++ b/sci-biology/SPAdes/SPAdes-3.11.1.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python{2_7,3_{4,5}} ) + +inherit eutils toolchain-funcs + +DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage" +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 -> ${P}_manual.html + http://spades.bioinf.spbau.ru/release${PV}/dipspades_manual.html -> ${P}_dipspades_manual.html + http://spades.bioinf.spbau.ru/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html + http://spades.bioinf.spbau.ru/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND=" + sys-libs/zlib + app-arch/bzip2 + dev-python/regex" +RDEPEND="${DEPEND}" +# BUG: +# SPAdes uses bundled while modified copy of dev-libs/boost (only headers are used, +# not *.so or *.a are even used) +# +# BUG: "${S}"/ext/src/ contains plenty of bundled 3rd-party tools. Drop them all and properly DEPEND on their +# existing packages +# nlopt +# llvm +# python_libs +# bamtools +# ConsensusCore +# ssw +# jemalloc +# htrie +# getopt_pp +# cppformat +# cityhash +# samtools +# bwa + +# BUG: "${S}"/ext/tools/ contains even two version of bwa, being installed as bwa-spades binary? +# bwa-0.7.12 +# bwa-0.6.2 + +pkg_pretend() { + if [[ ${MERGE_TYPE} != binary ]]; then + if [[ $(tc-getCXX) == *g++ ]] ; then + if [[ $(gcc-major-version) == 4 && $(gcc-minor-version) -lt 7 || $(gcc-major-version) -lt 4 ]] ; then + eerror "You need at least sys-devel/gcc-4.7.0" + die "You need at least sys-devel/gcc-4.7.0" + fi + fi + fi +} + +src_compile(){ + PREFIX="${ED}"/usr ./spades_compile.sh || die +} + +src_install(){ + # BUG: move *.py files to standard site-packages/ subdirectories + insinto /usr/share/"${PN}" + dodoc "${DISTDIR}"/${P}_*manual.html +} |