sci-biology/mRNAmarkup: new package

Package-Manager: portage-2.2.26

5 files changed, 137 insertions, 0 deletions

diff --git a/sci-biology/mRNAmarkup/ChangeLog b/sci-biology/mRNAmarkup/ChangeLog
new file mode 100644
index 000000000..e5311ca5b
--- /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/Manifest b/sci-biology/mRNAmarkup/Manifest
new file mode 100644
index 000000000..f09fec6e7
--- /dev/null
+++ b/sci-biology/mRNAmarkup/Manifest
@@ -0,0 +1,2 @@
+DIST mRNAmarkup-10-3-2013.tar.gz 225283371 SHA256 4fce294745dde0e55c0dda71c9c186d2372c28850d26cc7f4db68b23278f84a1 SHA512 bf752ed2459bb01ddb6d982a7aee4417634a52c42be5eda56f680aaf77e5e37c6feb3199f03784e754d95a417b9cda3eff83e47c31a733365f25e93a4c412303 WHIRLPOOL a3905f30aeda2980b803a50734529d4eca8b216398eb6db1b9d38bc372b5470971e50b87cfffa59c7d84c64333c5b6422facbe4574947f2f170ad28291b31f14
+DIST mRNAmarkup-4-8-2015.tar.gz 192523324 SHA256 51baed40d6ca3a4c7421068158289bce37d3b600c75639deef8287de759b92eb SHA512 caf537f98bf3a11e28e47a6e6833eb70e1f810cd1ad3033d30f7a941fb136f08e243abb373a105a86191ba939fc56537967ef598f714d1a8f40f6ee9967732b3 WHIRLPOOL 71dce3091d9766b56b9e0ff6c320787788c3794fa2a56fb2ee43d5c08e539bd55be9f68cebbdcaddc8c1506232f0beb3a221f58901f0033e4299b4d619a4b12d
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"
+}
diff --git a/sci-biology/mRNAmarkup/mRNAmarkup-1.1.ebuild b/sci-biology/mRNAmarkup/mRNAmarkup-1.1.ebuild
new file mode 100644
index 000000000..c0f7579ab
--- /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 000000000..2bc893037
--- /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>