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commit: 8ef2d0632281aeb653b62b10b8da00f22f9cc62d |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Sun Jan 29 18:08:40 2017 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Sun Jan 29 18:08:40 2017 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8ef2d063 |
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|
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sci-biology/SPAdes: version bump, remove old, src_install actually does also src_compile |
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|
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Upstream contacted to split compile and install steps into separate procedures. |
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The Gentoo package should be probably renamed to all lowercase letters. |
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Hierarchy in /usr/share/spades/ is a bit awkward. |
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|
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Package-Manager: Portage-2.3.3, Repoman-2.3.1 |
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|
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.../{SPAdes-3.5.0.ebuild => SPAdes-3.9.1.ebuild} | 23 +++++++++++----------- |
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sci-biology/SPAdes/metadata.xml | 7 ++++++- |
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2 files changed, 17 insertions(+), 13 deletions(-) |
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|
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diff --git a/sci-biology/SPAdes/SPAdes-3.5.0.ebuild b/sci-biology/SPAdes/SPAdes-3.9.1.ebuild |
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similarity index 64% |
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rename from sci-biology/SPAdes/SPAdes-3.5.0.ebuild |
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rename to sci-biology/SPAdes/SPAdes-3.9.1.ebuild |
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index 45cb010..1a5a5d5 100644 |
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--- a/sci-biology/SPAdes/SPAdes-3.5.0.ebuild |
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+++ b/sci-biology/SPAdes/SPAdes-3.9.1.ebuild |
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@@ -1,4 +1,4 @@ |
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-# Copyright 1999-2016 Gentoo Foundation |
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+# Copyright 1999-2017 Gentoo Foundation |
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# Distributed under the terms of the GNU General Public License v2 |
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# $Id$ |
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|
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@@ -11,8 +11,8 @@ inherit eutils toolchain-funcs |
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DESCRIPTION="De novo de Bruijn genome assembler (bacteria to fungi) or uneven coverage" |
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HOMEPAGE="http://bioinf.spbau.ru/en/spades" |
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SRC_URI=" |
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- http://spades.bioinf.spbau.ru/release3.5.0/SPAdes-3.5.0.tar.gz |
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- http://spades.bioinf.spbau.ru/release3.5.0/manual.html" |
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+ http://spades.bioinf.spbau.ru/release${PV}/SPAdes-${PV}.tar.gz |
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+ http://spades.bioinf.spbau.ru/release${PV}/manual.html -> ${P}_manual.html" |
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|
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LICENSE="GPL-2" |
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SLOT="0" |
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@@ -37,14 +37,13 @@ pkg_pretend() { |
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fi |
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} |
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|
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-src_prepare(){ |
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- insinto /usr/share/doc/SPAdes |
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- dodoc "${DISTDIR}"/manual.html |
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-} |
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+#src_compile(){ |
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+# # grr, it actually also installs the files into $DESTDIR but that is purged before pkg_qmerge starts |
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+# PREFIX="${D}"/usr ./spades_compile.sh || die |
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+#} |
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|
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-src_compile(){ |
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- # grr, it actually also installs the files into $PREFIX |
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- PREFIX="${D}"/usr ./spades_compile.sh || die |
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+src_install(){ |
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+ PREFIX="${ED}"/usr ./spades_compile.sh || die |
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+ insinto /usr/share/"${PN}" |
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+ dodoc "${DISTDIR}"/manual.html |
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} |
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- |
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-# BUG: contents of "${D}" do not propagate during qmerge? |
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|
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diff --git a/sci-biology/SPAdes/metadata.xml b/sci-biology/SPAdes/metadata.xml |
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index 1699e58..4baa308 100644 |
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--- a/sci-biology/SPAdes/metadata.xml |
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+++ b/sci-biology/SPAdes/metadata.xml |
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@@ -5,8 +5,13 @@ |
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<email>mmokrejs@×××××××××××××××.cz</email> |
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<name>Martin Mokrejs</name> |
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</maintainer> |
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-<maintainer type="project"> |
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+ <maintainer type="project"> |
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<email>sci-biology@g.o</email> |
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<name>Gentoo Biology Project</name> |
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</maintainer> |
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+ <longdescription> |
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+ truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads. |
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+ hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp. |
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+ dipspades is assembly module for highly polymorphic diploid genomes |
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+ </longdescription> |
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</pkgmetadata> |
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