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# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=3
inherit webapp eutils perl-module
[ "$PV" == "9999" ] && inherit git-2
DESCRIPTION="EST assembly+annotation: a perl-based analysis pipeline including php-based web interface"
HOMEPAGE="http://cichlid.umd.edu/est2uni/download.php"
if [ "$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
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
http://www.geneontology.org/doc/GO.terms_and_ids"
KEYWORDS="~amd64 ~x86"
fi
LICENSE="GPL-3"
IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
sci-biology/lucy
sci-biology/cap3-bin
sci-biology/estscan
<sci-biology/hmmer-3.0
sci-biology/phred
sci-biology/seqclean
sci-biology/repeatmasker
sci-biology/tgicl
sci-biology/ncbi-tools
sci-biology/bioperl
sci-biology/exonerate
dev-perl/go-perl
www-servers/apache
>=dev-db/mysql-4.1
<dev-lang/php-5.3"
S="${WORKDIR}"/est2uni
src_prepare(){
for f in "${FILESDIR}"/9999-*.pm.patch; do
cd perl; epatch $f || die "Failed to apply patch $f"
done
cd ../php || die "Failed to chdir to ../php"
epatch "${FILESDIR}"/configuration.php.patch || die "Failed to apply config patch for VHOSTS setup"
}
src_compile(){
"$(tc-getCC)" external_software/sputnik/sputnik.c -o external_software/sputnik/sputnik
}
src_install(){
mkdir -p "${D}"/opt/est2uni
mv external_software/sputnik/sputnik "${D}"/opt/est2uni || die
chmod a+rx perl/*.pl perl/*.pm || die
mv perl/* "${D}"/opt/est2uni || die
doenvd "${FILESDIR}"/99est2uni || die
mkdir -p "${D}"/usr/share/webapps/"${PN}"/"${PV}"/htdocs
cp -r php/* "${D}"/usr/share/webapps/"${PN}"/"${PV}"/htdocs || die
mkdir -p "${D}"/opt/est2uni/test_data || die
mv test_data/* "${D}"/opt/est2uni/test_data || die
# mkdir -p "${D}"/usr/share/"${PN}" || die
# mv test_data "${D}"/usr/share/"${PN}" || die
perl-module_src_install || die
webapp_src_preinst
webapp_postinst_txt en "${S}"/README
webapp_src_install
# mkdir -p /var/www/localhost/htdocs/est2uni/est2uni/temp
# mkdir -p /var/www/localhost/htdocs/est2uni/est2uni/blast
# cp "${DISTDIR}"/UniVec_Core "${DISTDIR}"/UniVec "${D}"/usr/share/ncbi/data/ || die
einfo "Please follow the pipeline installation and web configuration docs at"
einfo "http://cichlid.umd.edu/est2uni/install.php"
einfo ""
einfo "Example changes to the config file are in ${FILESDIR}/configuration.php.patch"
einfo ""
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"
einfo "release from 2007 or so."
einfo "Possible fixes and stuff to read:"
einfo "https://listas.upv.es/pipermail/est2uni/2008-January/000069.html"
einfo "https://listas.upv.es/pipermail/est2uni/2008-March/000103.html"
einfo "https://listas.upv.es/pipermail/est2uni/2008-March/000101.html"
einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000135.html"
einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000131.html"
einfo "https://listas.upv.es/pipermail/est2uni/2008-February/000070.html"
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 ""
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"
}
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