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| author |   Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-01-29 19:08:40 +0100 |
|---|---|---|
| committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-01-29 19:08:40 +0100 |
| commit | 8ef2d0632281aeb653b62b10b8da00f22f9cc62d (patch) | |
| tree | 2497731672d0e030073e7e2ef6481ee4d8fabd90 /sci-biology/SPAdes | |
| parent | sci-biology/pb-honey: QA fixes (diff) | |
| download | sci-8ef2d0632281aeb653b62b10b8da00f22f9cc62d.tar.gz sci-8ef2d0632281aeb653b62b10b8da00f22f9cc62d.tar.bz2 sci-8ef2d0632281aeb653b62b10b8da00f22f9cc62d.zip | |
sci-biology/SPAdes: version bump, remove old, src_install actually does also src_compile
Upstream contacted to split compile and install steps into separate procedures.
The Gentoo package should be probably renamed to all lowercase letters.
Hierarchy in /usr/share/spades/ is a bit awkward.
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Diffstat (limited to 'sci-biology/SPAdes')
| -rw-r--r-- | sci-biology/SPAdes/Manifest | 4 | ||||
| -rw-r--r-- | sci-biology/SPAdes/SPAdes-3.9.1.ebuild (renamed from sci-biology/SPAdes/SPAdes-3.5.0.ebuild) | 23 | ||||
| -rw-r--r-- | sci-biology/SPAdes/metadata.xml | 7 |
3 files changed, 19 insertions, 15 deletions
diff --git a/sci-biology/SPAdes/Manifest b/sci-biology/SPAdes/Manifest index 1d59e5c69..abaa184aa 100644 --- a/sci-biology/SPAdes/Manifest +++ b/sci-biology/SPAdes/Manifest @@ -1,2 +1,2 @@ -DIST SPAdes-3.5.0.tar.gz 8803835 SHA256 dfc23d5ab0fdde72b50bff016e76ab2db4f3659bf149874f85859b5c79bbec57 SHA512 05531a357f88948ba30dd5b1d5dd23d12d0b192ae78bd74d0bf6fffe841c2e81736bef756686a6d4dfc561c85b9bcd76653c8f0554a6c42b837d12ee436dc882 WHIRLPOOL 4dd2ff6f4dd75dae6d63ac2d47e32fc5237ca0cb54069d3a10a9f4607bcc499925b228bbbfd5722fb18ff565e8ff825890e20c825a21022dc3d0bfd2a95f53e4 -DIST manual.html 50562 SHA256 4d63ccb5be9d10936238f2910743a96a75dba978828f18959fafa97195ddf560 SHA512 c1fe2f2400600a0f37b7bfcf43d8a8448dda6ceab79737444e8054f2af5b8fdbed0c809d7186d3e22ad840e0770821aabeaa203deacc4d27a45e05d4e4709c45 WHIRLPOOL 1ab728ec471b7a1073575b18dbf5caeae0bc9bc5a6043e03ed29806840d25619f62d0587a87d6f5f187e2f1c77c652c4a81502b537ce3e6c07978a704fac8e63 +DIST SPAdes-3.9.1.tar.gz 6873127 SHA256 da8e923fb1d5c1508b11a2928a8ca3efd8bf22a723d257f0e511c033f74022d8 SHA512 c0fc6cd64c89f817c753de5b9b6b9696a21f6b2fc089febd5a5a225076d245000eb6739f4bbf67af12b679d4a9788ece684d16f0562dd15f2d5c771492b94634 WHIRLPOOL b3d052dc24a9b56b62cbbe9c69b85790e9e49dae7faef3ec4cbb12e08253120eea98f9d7901e5634f33430c3e038ed590f07a02cc193843fc0f33cf404a4d4a0 +DIST SPAdes-3.9.1_manual.html 59108 SHA256 db823fc5f903b15e3fbb766ca1ffd8dcd499a31bdbb6b90bcd99cf26d35c655b SHA512 b0dfec879322f9e47aa646b61dda434504f1e4312ddd986d243bc60dcef3d5d89814f4e7237a4b6501588ce0df49c95ca10712ff4b18b4440ad8ab2d9783f691 WHIRLPOOL b9f2f961bf8d51a4638b37c1335f2c8e6b8b7a15039c82ae98d38321afc8cc1d78515eeabd83d88fafc6fe71f5c07d33e0c6051e89378e2fd1f90db04e357987 diff --git a/sci-biology/SPAdes/SPAdes-3.5.0.ebuild b/sci-biology/SPAdes/SPAdes-3.9.1.ebuild index 45cb01053..1a5a5d584 100644 --- a/sci-biology/SPAdes/SPAdes-3.5.0.ebuild +++ b/sci-biology/SPAdes/SPAdes-3.9.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ @@ -11,8 +11,8 @@ inherit eutils toolchain-funcs DESCRIPTION="De novo de Bruijn genome assembler (bacteria to fungi) or uneven coverage" HOMEPAGE="http://bioinf.spbau.ru/en/spades" SRC_URI=" - http://spades.bioinf.spbau.ru/release3.5.0/SPAdes-3.5.0.tar.gz - http://spades.bioinf.spbau.ru/release3.5.0/manual.html" + http://spades.bioinf.spbau.ru/release${PV}/SPAdes-${PV}.tar.gz + http://spades.bioinf.spbau.ru/release${PV}/manual.html -> ${P}_manual.html" LICENSE="GPL-2" SLOT="0" @@ -37,14 +37,13 @@ pkg_pretend() { fi } -src_prepare(){ - insinto /usr/share/doc/SPAdes - dodoc "${DISTDIR}"/manual.html -} +#src_compile(){ +# # grr, it actually also installs the files into $DESTDIR but that is purged before pkg_qmerge starts +# PREFIX="${D}"/usr ./spades_compile.sh || die +#} -src_compile(){ - # grr, it actually also installs the files into $PREFIX - PREFIX="${D}"/usr ./spades_compile.sh || die +src_install(){ + PREFIX="${ED}"/usr ./spades_compile.sh || die + insinto /usr/share/"${PN}" + dodoc "${DISTDIR}"/manual.html } - -# BUG: contents of "${D}" do not propagate during qmerge? diff --git a/sci-biology/SPAdes/metadata.xml b/sci-biology/SPAdes/metadata.xml index 1699e58b2..4baa30821 100644 --- a/sci-biology/SPAdes/metadata.xml +++ b/sci-biology/SPAdes/metadata.xml @@ -5,8 +5,13 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> -<maintainer type="project"> + <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <longdescription> + truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads. + hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp. + dipspades is assembly module for highly polymorphic diploid genomes + </longdescription> </pkgmetadata> |