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author | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2016-01-05 10:55:00 +0100 |
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committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2016-01-05 10:55:00 +0100 |
commit | b6b6962693d703889cd35ff7c66e2c268f01a793 (patch) | |
tree | b9000ec0b9c8a0806b7425ae0d865e26bcbd1915 /sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild | |
parent | sci-biology/MuSeqBox: new package (diff) | |
download | sci-b6b6962693d703889cd35ff7c66e2c268f01a793.tar.gz sci-b6b6962693d703889cd35ff7c66e2c268f01a793.tar.bz2 sci-b6b6962693d703889cd35ff7c66e2c268f01a793.zip |
sci-biology/mRNAmarkup: new package
Package-Manager: portage-2.2.26
Diffstat (limited to 'sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild')
-rw-r--r-- | sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild | 58 |
1 files changed, 58 insertions, 0 deletions
diff --git a/sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild b/sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild new file mode 100644 index 000000000..eb903abab --- /dev/null +++ b/sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Transcript annotation workflow" +HOMEPAGE="http://brendelgroup.org/bioinformatics2go/mRNAmarkup.php" +SRC_URI="http://www.brendelgroup.org/bioinformatics2go/Download/mRNAmarkup-10-3-2013.tar.gz" # 215MB + +# 0README in version 20131003 says it is 1.0 + +LICENSE="mRNAmarkup" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +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}"/"${PN}" + +src_prepare(){ + sed -e \ + "s#configfile=$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" +} |