commit: 0069fa855baffaac7a79f53467dc8258eaaa5883 Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Tue Jan 19 11:06:34 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Tue Jan 19 11:06:47 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0069fa85
sci-biology/mRNAmarkup: version bump, fix fetch Package-Manager: Portage-3.0.13, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> profiles/package.mask | 1 - sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild | 57 ---------------------- ...rkup-1.1.ebuild => mRNAmarkup-5.21.2019.ebuild} | 12 ++--- 3 files changed, 5 insertions(+), 65 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 650fb6a4b..43fa4e9d6 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -86,4 +86,3 @@ sci-biology/mavid sci-biology/MeV sci-biology/MolBioLib sci-biology/mreps -sci-biology/mRNAmarkup diff --git a/sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild b/sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild deleted file mode 100644 index dbdc3e368..000000000 --- a/sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -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#$installdir/bin/ESTScan.conf#/usr/share/mRNAmarkup/etc/ESTScan.conf#" \ - -i bin/mRNAmarkup.orig -} - -src_compile(){ - cd src - emake -} - -src_install(){ - mv bin/mRNAmarkup.orig bin/mRNAmarkup - sed -e 's#INSTALLDIR#/usr/share/mRNAmarkup/etc/#' -i bin/mRNAmarkup - dobin bin/mRNAmarkup bin/*.pl bin/dnatopro bin/genestat - # TODO: there are some more files in bin/ , sigh! - insinto /usr/share/mRNAmarkup/etc - mv mRNAmarkup.conf.orig mRNAmarkup.conf - doins mRNAmarkup.conf - doins bin/ESTScan.conf - dodoc 0README INSTALL -} - -pkg_postinst(){ - einfo "Please obtain a local copy of NCBI CDD dastabase" -} diff --git a/sci-biology/mRNAmarkup/mRNAmarkup-1.1.ebuild b/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild similarity index 89% rename from sci-biology/mRNAmarkup/mRNAmarkup-1.1.ebuild rename to sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild index f68f0d335..fb37b69f9 100644 --- a/sci-biology/mRNAmarkup/mRNAmarkup-1.1.ebuild +++ b/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild @@ -1,18 +1,15 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 DESCRIPTION="Transcript annotation workflow" HOMEPAGE="http://brendelgroup.org/bioinformatics2go/mRNAmarkup.php"; -SRC_URI="http://www.brendelgroup.org/bioinformatics2go/Download/mRNAmarkup-4-8-2015.tar.gz"; # 184MB - -# mRNAmarkup-4-8-2015.tar.gz is 1.1 version +SRC_URI="http://www.brendelgroup.org/bioinformatics2go/Download/mRNAmarkup-${PV//./-}.tar.gz"; # 184MB LICENSE="mRNAmarkup" SLOT="0" KEYWORDS="~amd64" -IUSE="" DEPEND=" sci-biology/ncbi-tools++ @@ -24,9 +21,10 @@ DEPEND=" # has a slightly modified estscan copy in src/contributed RDEPEND="${DEPEND}" -S="${WORKDIR}"/"${PN}" +S="${WORKDIR}/${PN}" src_prepare(){ + default sed -e \ "s#configfile=$installdir/mRNAmarkup.conf#configfile=/usr/share/mRNAmarkup/etc/mRNAmarkup.conf#" \ -i bin/mRNAmarkup.orig || die
