sci-biology/est2uni: Bump to EAPI=4, remove unnecessary bits

(Portage version: 2.2.0_alpha107/git/Linux x86_64, unsigned Manifest commit)

3 files changed, 47 insertions, 41 deletions

diff --git a/sci-biology/est2uni/ChangeLog b/sci-biology/est2uni/ChangeLog
index b4090e1ca..e58990663 100644
--- a/sci-biology/est2uni/ChangeLog
+++ b/sci-biology/est2uni/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/est2uni
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  22 May 2012; Justin Lecher <jlec@gentoo.org> est2uni-0.27.ebuild,
+  est2uni-9999.ebuild:
+  Bump to EAPI=4, remove unnecessary bits
+
   12 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   est2uni-9999.ebuild:
   added configuration.php.patch for VHOSTS setup files/configuration.php.patch
diff --git a/sci-biology/est2uni/est2uni-0.27.ebuild b/sci-biology/est2uni/est2uni-0.27.ebuild
index 7252b2f8a..063e02a95 100644
--- a/sci-biology/est2uni/est2uni-0.27.ebuild
+++ b/sci-biology/est2uni/est2uni-0.27.ebuild
@@ -1,12 +1,12 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=3
+EAPI=4
 
 inherit eutils perl-module webapp
 
-DESCRIPTION="EST assembly+annotation: a perl-based analysis pipeline including php-based web interface"
+DESCRIPTION="Perl-based analysis pipeline including php-based web interface"
 HOMEPAGE="http://cichlid.umd.edu/est2uni/download.php"
 SRC_URI="
 	http://cichlid.umd.edu/est2uni/est2uni_0.27.tar.gz
@@ -22,27 +22,27 @@ IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}
-	sci-biology/lucy
+	>=dev-db/mysql-4.1
+	dev-lang/php:5.3
+	dev-perl/go-perl
+	sci-biology/bioperl
 	sci-biology/cap3-bin
 	sci-biology/estscan
-	<sci-biology/hmmer-3
+	sci-biology/exonerate
+	<sci-biology/hmmer-3.0
+	sci-biology/lucy
+	sci-biology/ncbi-tools
 	sci-biology/phred
-	sci-biology/seqclean
 	sci-biology/repeatmasker
+	sci-biology/seqclean
 	sci-biology/tgicl
-	sci-biology/ncbi-tools
-	sci-biology/bioperl
-	sci-biology/exonerate
-	www-servers/apache
-	>=dev-db/mysql-4.1
-	<dev-lang/php-5.3"
-#	perl-gcpan/go-perl
+	www-servers/apache"
 
 S="${WORKDIR}"/est2uni
 
 src_prepare(){
 	for f in "${FILESDIR}"/*.pm.patch "${FILESDIR}"/tgicl_files.patch; do
-		cd perl; epatch $f || die "Failed to patch $f"
+		cd perl; epatch $f
 	done
 }
 
@@ -57,7 +57,7 @@ src_install(){
 	chmod a+rx perl/*.pl perl/*.pm || die
 	mv perl/* "${D}"/opt/est2uni || die
 
-	doenvd "${FILESDIR}"/99est2uni || die
+	doenvd "${FILESDIR}"/99est2uni
 
 	mkdir -p "${D}"/usr/share/webapps/"${PN}"/"${PV}"/htdocs
 	cp -r php/* "${D}"/usr/share/webapps/"${PN}"/"${PV}"/htdocs || die
@@ -90,10 +90,10 @@ src_install(){
 	einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000129.html"
 	einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000128.html"
 	einfo "https://listas.upv.es/pipermail/est2uni/2008-May/000139.html"
-	einfo ""
+	echo ""
 	einfo "Current code is at http://bioinf.comav.upv.es/git///?p=est2uni;a=summary"
 }
 
 pkg_postinst(){
-	webapp_pkg_postinst || die "webapp_pkg_postinst failed"
+	webapp_pkg_postinst
 }
diff --git a/sci-biology/est2uni/est2uni-9999.ebuild b/sci-biology/est2uni/est2uni-9999.ebuild
index b3be36338..bb491c482 100644
--- a/sci-biology/est2uni/est2uni-9999.ebuild
+++ b/sci-biology/est2uni/est2uni-9999.ebuild
@@ -1,20 +1,21 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=3
+EAPI=4
 
-inherit webapp eutils perl-module
+[ "$PV" == "9999" ] && _GIT=git-2
 
-[ "$PV" == "9999" ] && inherit git-2
+inherit eutils ${_GIT} perl-module webapp
 
-DESCRIPTION="EST assembly+annotation: a perl-based analysis pipeline including php-based web interface"
+DESCRIPTION="Perl-based analysis pipeline including php-based web interface"
 HOMEPAGE="http://cichlid.umd.edu/est2uni/download.php"
 if [ "$PV" == "9999" ]; then
 	EGIT_REPO_URI="git://gitolite@bioinfo.comav.upv.es:2203/est2uni.git"
 	KEYWORDS=""
 else
-	SRC_URI="http://cichlid.umd.edu/est2uni/est2uni.tar.gz
+	SRC_URI="
+		http://cichlid.umd.edu/est2uni/est2uni.tar.gz
 		ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec
 		ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec_Core
 		http://www.geneontology.org/ontology/gene_ontology.obo
@@ -22,39 +23,40 @@ else
 	KEYWORDS="~amd64 ~x86"
 fi
 
+SLOT="0"
 LICENSE="GPL-3"
 IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}
-	sci-biology/lucy
+	>=dev-db/mysql-4.1
+	dev-lang/php:5.3
+	dev-perl/go-perl
+	sci-biology/bioperl
 	sci-biology/cap3-bin
 	sci-biology/estscan
+	sci-biology/exonerate
 	<sci-biology/hmmer-3.0
+	sci-biology/lucy
+	sci-biology/ncbi-tools
 	sci-biology/phred
-	sci-biology/seqclean
 	sci-biology/repeatmasker
+	sci-biology/seqclean
 	sci-biology/tgicl
-	sci-biology/ncbi-tools
-	sci-biology/bioperl
-	sci-biology/exonerate
-	dev-perl/go-perl
-	www-servers/apache
-	>=dev-db/mysql-4.1
-	<dev-lang/php-5.3"
+	www-servers/apache"
 
 S="${WORKDIR}"/est2uni
 
 src_prepare(){
 	for f in "${FILESDIR}"/9999-*.pm.patch; do
-		cd perl; epatch $f || die "Failed to apply patch $f"
+		cd perl; epatch $f
 	done
 	cd ../php || die "Failed to chdir to ../php"
-	epatch "${FILESDIR}"/configuration.php.patch || die "Failed to apply config patch for VHOSTS setup"
+	epatch "${FILESDIR}"/configuration.php.patch
 }
 
 src_compile(){
-	"$(tc-getCC)" external_software/sputnik/sputnik.c -o external_software/sputnik/sputnik
+	$(tc-getCC) ${CFLAGS} ${LDFLAGS} external_software/sputnik/sputnik.c -o external_software/sputnik/sputnik || die
 }
 
 src_install(){
@@ -64,7 +66,7 @@ src_install(){
 	chmod a+rx perl/*.pl perl/*.pm || die
 	mv perl/* "${D}"/opt/est2uni || die
 
-	doenvd "${FILESDIR}"/99est2uni || die
+	doenvd "${FILESDIR}"/99est2uni
 
 	mkdir -p "${D}"/usr/share/webapps/"${PN}"/"${PV}"/htdocs
 	cp -r php/* "${D}"/usr/share/webapps/"${PN}"/"${PV}"/htdocs || die
@@ -85,9 +87,9 @@ src_install(){
 
 	einfo "Please follow the pipeline installation and web configuration docs at"
 	einfo "http://cichlid.umd.edu/est2uni/install.php"
-	einfo ""
+	echo ""
 	einfo "Example changes to the config file are in ${FILESDIR}/configuration.php.patch"
-	einfo ""
+	echo ""
 	einfo "BEWARE the software is not maintained anymore by upstream but I do not"
 	einfo "know any better available (replaced by ngs_backbone which has no web"
 	einfo "interface yet). Consider using latest svn checkout instead of 0.27"
@@ -102,10 +104,10 @@ src_install(){
 	einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000129.html"
 	einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000128.html"
 	einfo "https://listas.upv.es/pipermail/est2uni/2008-May/000139.html"
-	einfo ""
+	echo ""
 	einfo "Current code is at http://bioinf.comav.upv.es/git///?p=est2uni;a=summary"
 }
 
 pkg_postinst(){
-	webapp_pkg_postinst || die "webapp_pkg_postinst failed"
+	webapp_pkg_postinst
 }