From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 0B5C51396D0 for ; Thu, 7 Sep 2017 20:49:46 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 358D4E0D88; Thu, 7 Sep 2017 20:49:45 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 09129E0D88 for ; Thu, 7 Sep 2017 20:49:45 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 0E0D63402FE for ; Thu, 7 Sep 2017 20:49:44 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id A555B8F31 for ; Thu, 7 Sep 2017 20:49:42 +0000 (UTC) From: "David Seifert" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "David Seifert" Message-ID: <1504817350.539fae1fd1daad0dc762aaa66fcb6fcec4d46bdc.soap@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/TransDecoder/files/, sci-biology/TransDecoder/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild sci-biology/TransDecoder/files/TransDecoder-2.0.1__fix_paths.patch X-VCS-Directories: sci-biology/TransDecoder/files/ sci-biology/TransDecoder/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: 539fae1fd1daad0dc762aaa66fcb6fcec4d46bdc X-VCS-Branch: master Date: Thu, 7 Sep 2017 20:49:42 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 944651d3-5330-49d2-91a9-61c68189f82b X-Archives-Hash: 3ae4d49d0f7014d761d2daf5437415d4 commit: 539fae1fd1daad0dc762aaa66fcb6fcec4d46bdc Author: David Seifert gentoo org> AuthorDate: Thu Sep 7 20:49:10 2017 +0000 Commit: David Seifert gentoo 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}"; - -