commit: 6f631fd58c22a7c42ece339ec8d5ead6d53f55fe Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Thu Sep 7 20:47:27 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Thu Sep 7 20:47:34 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6f631fd5
sci-biology/TransDecoder: Fix double-prefix Closes: https://bugs.gentoo.org/show_bug.cgi?id=587702 Package-Manager: Portage-2.3.8, Repoman-2.3.3 sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild | 68 +++++++++------------- .../TransDecoder/files/pfam_runner.pl.patch | 4 +- 2 files changed, 31 insertions(+), 41 deletions(-) diff --git a/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild b/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild index bb592938e..6b462ff90 100644 --- a/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild +++ b/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild @@ -1,45 +1,47 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=6 -[ "$PV" == "9999" ] && inherit git-r3 - -PERL_EXPORT_PHASE_FUNCTIONS=no -inherit perl-module eutils toolchain-funcs +inherit perl-functions toolchain-funcs DESCRIPTION="Extract ORF/CDS regions from FASTA sequences" HOMEPAGE="http://transdecoder.github.io"; -if [ "$PV" == "9999" ]; then + +if [[ ${PV} == *9999 ]]; then + inherit git-r3 EGIT_REPO_URI="https://github.com/TransDecoder/TransDecoder.git"; - KEYWORDS="" else - SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/v"${PV}".tar.gz -> ${P}.tar.gz" + SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/v${PV}.tar.gz -> ${P}.tar.gz" KEYWORDS="~amd64" - S="${WORKDIR}"/TransDecoder-"${PV}" fi LICENSE="BSD-BroadInstitute" SLOT="0" IUSE="" -DEPEND="" +DEPEND="dev-lang/perl:=" RDEPEND="${DEPEND} sci-biology/cd-hit sci-biology/parafly sci-biology/ffindex" -src_prepare(){ - rm -rf transdecoder_plugins/cd-hit +src_prepare() { + rm -rf transdecoder_plugins/cd-hit || die + local f p 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; + 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 "${FILESDIR}"/pfam_runner.pl.patch + eapply "${FILESDIR}"/"${P}"__fix_paths.patch + eapply "${FILESDIR}"/pfam_runner.pl.patch + + eapply_user } -src_compile(){ +src_compile() { einfo "Skipping compilation of bundled cd-hit code, nothing else to do" } @@ -48,37 +50,25 @@ src_compile(){ # thread in archives. You can get it from # http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin -src_install(){ +src_install() { dobin TransDecoder.Predict TransDecoder.LongOrfs + insinto /usr/share/${PN}/util doins util/*.pl - chmod -R a+rx "${D}"/"${EPREFIX}"/usr/share/${PN}/util || die + + chmod -R a+rx "${ED%/}"/usr/share/${PN}/util || die # 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 - # this is broken and installs into - # /scratch/mmokrejs/gentoo/var/tmp/portage/sci-biology/TransDecoder-2.1.0/image/scratch/mmokrejs/gentoo/scratch/mmokrejs/gentoo/usr/lib/perl5/vendor_perl/ - # instead of - # /scratch/mmokrejs/gentoo/var/tmp/portage/sci-biology/TransDecoder-2.1.0/image/scratch/mmokrejs/gentoo/usr/lib/perl5/vendor_perl/ - insinto ${VENDOR_LIB}/${PN} - doins PerlLib/*.pm + rm -rf util/bin || die + + perl_domodule -C ${PN} 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(){ +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" diff --git a/sci-biology/TransDecoder/files/pfam_runner.pl.patch b/sci-biology/TransDecoder/files/pfam_runner.pl.patch index fbc6f6d92..1e8b96cc7 100644 --- a/sci-biology/TransDecoder/files/pfam_runner.pl.patch +++ b/sci-biology/TransDecoder/files/pfam_runner.pl.patch @@ -1,5 +1,5 @@ ---- util/pfam_runner.pl 2015-01-09 11:22:55.000000000 +0100 -+++ util/pfam_runner.pl 2015-01-09 14:25:43.385838579 +0100 +--- a/util/pfam_runner.pl ++++ b/util/pfam_runner.pl @@ -24,7 +24,7 @@ my $workdir; my $verbose;
