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

[David Seifert]

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;