commit: 539fae1fd1daad0dc762aaa66fcb6fcec4d46bdc Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Thu Sep 7 20:49:10 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Thu Sep 7 20:49:10 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=539fae1f
sci-biology/TransDecoder: Remove old Package-Manager: Portage-2.3.8, Repoman-2.3.3 sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild | 82 ---------------------- .../files/TransDecoder-2.0.1__fix_paths.patch | 22 ------ 2 files changed, 104 deletions(-) diff --git a/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild b/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild deleted file mode 100644 index 1e5f1ad23..000000000 --- a/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild +++ /dev/null @@ -1,82 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -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/"${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}"/"${EPREFIX}"/usr/share/${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 - insinto ${VENDOR_LIB}/${PN} - doins PerlLib/*.pm - dodoc Release.Notes - einfo "Fetch on 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-2.0.1__fix_paths.patch b/sci-biology/TransDecoder/files/TransDecoder-2.0.1__fix_paths.patch deleted file mode 100644 index 0a6fca050..000000000 --- a/sci-biology/TransDecoder/files/TransDecoder-2.0.1__fix_paths.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- 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}"; - -
