[gentoo-commits] proj/sci:master commit in: sci-biology/TransDecoder/files/, sci-biology/TransDecoder/

[David Seifert]

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}";
- 
-