* [gentoo-commits] proj/sci:master commit in: sci-biology/mRNAmarkup/
@ 2016-01-05 9:56 Martin Mokrejs
0 siblings, 0 replies; 2+ messages in thread
From: Martin Mokrejs @ 2016-01-05 9:56 UTC (permalink / raw
To: gentoo-commits
commit: b6b6962693d703889cd35ff7c66e2c268f01a793
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 5 09:55:00 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 5 09:55:00 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b6b69626
sci-biology/mRNAmarkup: new package
Package-Manager: portage-2.2.26
sci-biology/mRNAmarkup/ChangeLog | 10 +++++
sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild | 58 ++++++++++++++++++++++++++++
sci-biology/mRNAmarkup/mRNAmarkup-1.1.ebuild | 58 ++++++++++++++++++++++++++++
sci-biology/mRNAmarkup/metadata.xml | 9 +++++
4 files changed, 135 insertions(+)
diff --git a/sci-biology/mRNAmarkup/ChangeLog b/sci-biology/mRNAmarkup/ChangeLog
new file mode 100644
index 0000000..e5311ca
--- /dev/null
+++ b/sci-biology/mRNAmarkup/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/mRNAmarkup
+# Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2
+# $Id$
+
+*mRNAmarkup-1.0 (05 Jan 2016)
+*mRNAmarkup-1.1 (05 Jan 2016)
+
+ 05 Jan 2016; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +mRNAmarkup-1.0.ebuild, +mRNAmarkup-1.1.ebuild, +metadata.xml:
+ sci-biology/mRNAmarkup: new package
diff --git a/sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild b/sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild
new file mode 100644
index 0000000..eb903ab
--- /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"
+}
diff --git a/sci-biology/mRNAmarkup/mRNAmarkup-1.1.ebuild b/sci-biology/mRNAmarkup/mRNAmarkup-1.1.ebuild
new file mode 100644
index 0000000..c0f7579
--- /dev/null
+++ b/sci-biology/mRNAmarkup/mRNAmarkup-1.1.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-4-8-2015.tar.gz" # 184MB
+
+# mRNAmarkup-4-8-2015.tar.gz is 1.1 version
+
+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/metadata.xml b/sci-biology/mRNAmarkup/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/mRNAmarkup/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mRNAmarkup/
@ 2022-12-01 22:01 Andrew Ammerlaan
0 siblings, 0 replies; 2+ messages in thread
From: Andrew Ammerlaan @ 2022-12-01 22:01 UTC (permalink / raw
To: gentoo-commits
commit: 68381f880ac18171246417b6dfc9c35a77d12232
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Dec 1 22:00:48 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Dec 1 22:00:48 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=68381f88
sci-biology/mRNAmarkup: treeclean
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild | 55 ----------------------
sci-biology/mRNAmarkup/metadata.xml | 12 -----
2 files changed, 67 deletions(-)
diff --git a/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild b/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild
deleted file mode 100644
index fb37b69f9..000000000
--- a/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# 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"
-}
diff --git a/sci-biology/mRNAmarkup/metadata.xml b/sci-biology/mRNAmarkup/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/mRNAmarkup/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 2+ messages in thread
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