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authorMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2018-01-09 23:03:02 +0100
committerMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2018-01-09 23:03:02 +0100
commit4dd7fc5f1806465684c1101c88021ab3e1993fa2 (patch)
tree4bcae8f623062e733cf3def2badbef953978b8eb
parentsci-biology/BRAKER: version bump (diff)
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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/Manifest5
-rw-r--r--sci-biology/SPAdes/SPAdes-3.11.1.ebuild72
2 files changed, 77 insertions, 0 deletions
diff --git a/sci-biology/SPAdes/Manifest b/sci-biology/SPAdes/Manifest
index 1e14b8e..f7c0aab 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 0000000..1842fca
--- /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
+}