[gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/mRNAmarkup/

[gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/mRNAmarkup/

[Andrew Ammerlaan]

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