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commit: 1a200d0a079c95ff7357a3581d1f43be63af802d |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Wed Mar 30 14:47:35 2016 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Wed Mar 30 14:47:35 2016 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1a200d0a |
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|
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sci-biology/TransDecoder: version bump |
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|
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Package-Manager: portage-2.2.28 |
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|
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sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild | 83 ++++++++++++++++++++++ |
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.../files/TransDecoder-2.1.0__fix_paths.patch | 22 ++++++ |
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2 files changed, 105 insertions(+) |
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|
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diff --git a/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild b/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild |
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new file mode 100644 |
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index 0000000..9fbcea5 |
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--- /dev/null |
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+++ b/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild |
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@@ -0,0 +1,83 @@ |
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+# Copyright 1999-2016 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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+EAPI=5 |
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+ |
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+[ "$PV" == "9999" ] && inherit git-r3 |
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+ |
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+PERL_EXPORT_PHASE_FUNCTIONS=no |
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+inherit perl-module eutils toolchain-funcs |
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+ |
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+DESCRIPTION="Extract ORF/CDS regions from FASTA sequences" |
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+HOMEPAGE="http://transdecoder.github.io" |
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+if [ "$PV" == "9999" ]; then |
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+ EGIT_REPO_URI="https://github.com/TransDecoder/TransDecoder.git" |
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+ KEYWORDS="" |
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+else |
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+ SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/v"${PV}".tar.gz -> ${P}.tar.gz" |
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+ KEYWORDS="~amd64" |
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+ S="${WORKDIR}"/TransDecoder-"${PV}" |
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+fi |
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+ |
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+LICENSE="BSD-BroadInstitute" |
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+SLOT="0" |
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+IUSE="" |
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+ |
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+DEPEND="" |
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+RDEPEND="${DEPEND} |
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+ sci-biology/cd-hit |
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+ sci-biology/parafly |
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+ sci-biology/ffindex" |
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+ |
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+src_prepare(){ |
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+ rm -rf transdecoder_plugins/cd-hit |
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+ for f in PerlLib/*.pm; do |
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+ p=`basename $f .pm`; |
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+ sed -e "s#use $p;#use TransDecoder::$p;#" -i PerlLib/*.pm util/*.pl TransDecoder.LongOrfs TransDecoder.Predict || die; |
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+ done |
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+ epatch "${FILESDIR}"/"${P}"__fix_paths.patch |
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+ epatch "${FILESDIR}"/pfam_runner.pl.patch |
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+} |
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+ |
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+src_compile(){ |
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+ einfo "Skipping compilation of bundled cd-hit code, nothing else to do" |
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+} |
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+ |
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+# avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see |
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+# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704" |
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+# thread in archives. You can get it from |
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+# http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin |
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+ |
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+src_install(){ |
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+ dobin TransDecoder.Predict TransDecoder.LongOrfs |
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+ insinto /usr/share/${PN}/util |
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+ doins util/*.pl |
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+ chmod -R a+rx "${D}"/usr/share/${PN}/util |
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+ # zap the bundled cdhit binaries copied from transdecoder_plugins/cdhit/ to util/bin |
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+ rm -rf util/bin |
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+ # |
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+ # * sci-biology/trinityrnaseq-20140413:0::science |
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+ # * /usr/bin/Fasta_reader.pm |
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+ # * /usr/bin/GFF3_utils.pm |
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+ # * /usr/bin/Gene_obj.pm |
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+ # * /usr/bin/Gene_obj_indexer.pm |
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+ # * /usr/bin/Longest_orf.pm |
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+ # * /usr/bin/Nuc_translator.pm |
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+ # * /usr/bin/TiedHash.pm |
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+ # |
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+ perl_set_version |
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+ insinto ${VENDOR_LIB}/${PN} |
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+ doins PerlLib/*.pm |
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+ # dodoc Release.Notes |
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+ einfo "Fetch your own Pfam-A.hmm (Pfam-AB.hmm is discontinued since 05/2015):" |
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+ einfo "wget --mirror -nH -nd ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz" |
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+ einfo "hmmpress Pfam-A.hmm.bin" |
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+} |
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+ |
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+pkg_postinst(){ |
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+ einfo "It is recommended to use TransDecoder with sci-biology/hmmer-3 or" |
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+ einfo "at least with NCBI blast from either:" |
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+ einfo " sci-biology/ncbi-blast+ (released more often) or from" |
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+ einfo " sci-biology/ncbi-toolkit++ (a huge bundle with releases and less frequent bugfixes)" |
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+} |
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|
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diff --git a/sci-biology/TransDecoder/files/TransDecoder-2.1.0__fix_paths.patch b/sci-biology/TransDecoder/files/TransDecoder-2.1.0__fix_paths.patch |
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new file mode 100644 |
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index 0000000..0a6fca0 |
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--- /dev/null |
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+++ b/sci-biology/TransDecoder/files/TransDecoder-2.1.0__fix_paths.patch |
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@@ -0,0 +1,22 @@ |
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+--- TransDecoder-2.0.1/TransDecoder.LongOrfs.ori 2015-11-19 21:05:53.340219051 +0100 |
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++++ TransDecoder-2.0.1/TransDecoder.LongOrfs 2015-11-19 21:20:44.870221380 +0100 |
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+@@ -64,7 +64,7 @@ |
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+ use TransDecoder::Fasta_reader; |
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+ use TransDecoder::Longest_orf; |
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+ |
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+-my $UTIL_DIR = "$FindBin::RealBin/util"; |
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++my $UTIL_DIR = "/usr/share/TransDecoder/util/"; |
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+ $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}"; |
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+ |
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+ |
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+--- TransDecoder-2.0.1/TransDecoder.Predict.ori 2015-11-19 21:06:04.280219080 +0100 |
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++++ TransDecoder-2.0.1/TransDecoder.Predict 2015-11-19 21:21:22.560221479 +0100 |
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+@@ -52,7 +52,7 @@ |
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+ use TransDecoder::Fasta_reader; |
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+ use TransDecoder::Longest_orf; |
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+ |
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+-my $UTIL_DIR = "$FindBin::RealBin/util"; |
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++my $UTIL_DIR = "/usr/share/TransDecoder/util/"; |
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+ $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}"; |
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+ |
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+ |