commit: 1a200d0a079c95ff7357a3581d1f43be63af802d Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Mar 30 14:47:35 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Mar 30 14:47:35 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1a200d0a
sci-biology/TransDecoder: version bump Package-Manager: portage-2.2.28 sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild | 83 ++++++++++++++++++++++ .../files/TransDecoder-2.1.0__fix_paths.patch | 22 ++++++ 2 files changed, 105 insertions(+) diff --git a/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild b/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild new file mode 100644 index 0000000..9fbcea5 --- /dev/null +++ b/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild @@ -0,0 +1,83 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +[ "$PV" == "9999" ] && inherit git-r3 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + +DESCRIPTION="Extract ORF/CDS regions from FASTA sequences" +HOMEPAGE="http://transdecoder.github.io"; +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="https://github.com/TransDecoder/TransDecoder.git"; + KEYWORDS="" +else + SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/v"${PV}".tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64" + S="${WORKDIR}"/TransDecoder-"${PV}" +fi + +LICENSE="BSD-BroadInstitute" +SLOT="0" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + sci-biology/cd-hit + sci-biology/parafly + sci-biology/ffindex" + +src_prepare(){ + rm -rf transdecoder_plugins/cd-hit + for f in PerlLib/*.pm; do + p=`basename $f .pm`; + sed -e "s#use $p;#use TransDecoder::$p;#" -i PerlLib/*.pm util/*.pl TransDecoder.LongOrfs TransDecoder.Predict || die; + done + epatch "${FILESDIR}"/"${P}"__fix_paths.patch + epatch "${FILESDIR}"/pfam_runner.pl.patch +} + +src_compile(){ + einfo "Skipping compilation of bundled cd-hit code, nothing else to do" +} + +# avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see +# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704" +# thread in archives. You can get it from +# http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin + +src_install(){ + dobin TransDecoder.Predict TransDecoder.LongOrfs + insinto /usr/share/${PN}/util + doins util/*.pl + chmod -R a+rx "${D}"/usr/share/${PN}/util + # zap the bundled cdhit binaries copied from transdecoder_plugins/cdhit/ to util/bin + rm -rf util/bin + # + # * sci-biology/trinityrnaseq-20140413:0::science + # * /usr/bin/Fasta_reader.pm + # * /usr/bin/GFF3_utils.pm + # * /usr/bin/Gene_obj.pm + # * /usr/bin/Gene_obj_indexer.pm + # * /usr/bin/Longest_orf.pm + # * /usr/bin/Nuc_translator.pm + # * /usr/bin/TiedHash.pm + # + perl_set_version + insinto ${VENDOR_LIB}/${PN} + doins PerlLib/*.pm + # dodoc Release.Notes + einfo "Fetch your own Pfam-A.hmm (Pfam-AB.hmm is discontinued since 05/2015):" + einfo "wget --mirror -nH -nd ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz"; + einfo "hmmpress Pfam-A.hmm.bin" +} + +pkg_postinst(){ + einfo "It is recommended to use TransDecoder with sci-biology/hmmer-3 or" + einfo "at least with NCBI blast from either:" + einfo " sci-biology/ncbi-blast+ (released more often) or from" + einfo " sci-biology/ncbi-toolkit++ (a huge bundle with releases and less frequent bugfixes)" +} 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 new file mode 100644 index 0000000..0a6fca0 --- /dev/null +++ b/sci-biology/TransDecoder/files/TransDecoder-2.1.0__fix_paths.patch @@ -0,0 +1,22 @@ +--- TransDecoder-2.0.1/TransDecoder.LongOrfs.ori 2015-11-19 21:05:53.340219051 +0100 ++++ TransDecoder-2.0.1/TransDecoder.LongOrfs 2015-11-19 21:20:44.870221380 +0100 +@@ -64,7 +64,7 @@ + use TransDecoder::Fasta_reader; + use TransDecoder::Longest_orf; + +-my $UTIL_DIR = "$FindBin::RealBin/util"; ++my $UTIL_DIR = "/usr/share/TransDecoder/util/"; + $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}"; + + +--- TransDecoder-2.0.1/TransDecoder.Predict.ori 2015-11-19 21:06:04.280219080 +0100 ++++ TransDecoder-2.0.1/TransDecoder.Predict 2015-11-19 21:21:22.560221479 +0100 +@@ -52,7 +52,7 @@ + use TransDecoder::Fasta_reader; + use TransDecoder::Longest_orf; + +-my $UTIL_DIR = "$FindBin::RealBin/util"; ++my $UTIL_DIR = "/usr/share/TransDecoder/util/"; + $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}"; + +
