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# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
DESCRIPTION="Transcript annotation workflow"
HOMEPAGE="http://brendelgroup.org/bioinformatics2go/mRNAmarkup.php"
SRC_URI="http://www.brendelgroup.org/bioinformatics2go/Download/mRNAmarkup-${PV//./-}.tar.gz" # 184MB
LICENSE="mRNAmarkup"
SLOT="0"
KEYWORDS="~amd64"
DEPEND="
sci-biology/ncbi-tools++
sci-biology/estscan"
# sci-biology/MuSeqBox has fetch-restrict and probably only works with old BLAST plaintex output
# but, mRNAmarkup/INSTALL says:
# 'For convenience, a copy of the MuSeqBox code distribution is included in directory src/contributed
#
# has a slightly modified estscan copy in src/contributed
RDEPEND="${DEPEND}"
S="${WORKDIR}/${PN}"
src_prepare(){
default
sed -e \
"s#configfile=$installdir/mRNAmarkup.conf#configfile=/usr/share/mRNAmarkup/etc/mRNAmarkup.conf#" \
-i bin/mRNAmarkup.orig || die
sed -e \
"s#$installdir/bin/ESTScan.conf#/usr/share/mRNAmarkup/etc/ESTScan.conf#" \
-i bin/mRNAmarkup.orig
}
src_compile(){
cd src
emake
}
src_install(){
mv bin/mRNAmarkup.orig bin/mRNAmarkup
sed -e 's#INSTALLDIR#/usr/share/mRNAmarkup/etc/#' -i bin/mRNAmarkup
dobin bin/mRNAmarkup bin/*.pl bin/dnatopro bin/genestat
# TODO: there are some more files in bin/ , sigh!
insinto /usr/share/mRNAmarkup/etc
mv mRNAmarkup.conf.orig mRNAmarkup.conf
doins mRNAmarkup.conf
doins bin/ESTScan.conf
dodoc 0README INSTALL
}
pkg_postinst(){
einfo "Please obtain a local copy of NCBI CDD dastabase"
}
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