[gentoo-commits] proj/sci:master commit in: sci-biology/cg-cat/

[gentoo-commits] proj/sci:master commit in: sci-biology/cg-cat/

[Martin Mokrejs]

commit:     0dc9a5177e72dac73b0ce8e8de20925b5e6df227
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Feb 10 17:05:29 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Feb 10 17:05:29 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0dc9a517

sci-biology/cg-cat: new package

Package-Manager: portage-2.2.26

 sci-biology/cg-cat/cg-cat-20150130.ebuild | 43 +++++++++++++++++++++++++++++++
 sci-biology/cg-cat/metadata.xml           | 12 +++++++++
 2 files changed, 55 insertions(+)

diff --git a/sci-biology/cg-cat/cg-cat-20150130.ebuild b/sci-biology/cg-cat/cg-cat-20150130.ebuild
new file mode 100644
index 0000000..39444ec
--- /dev/null
+++ b/sci-biology/cg-cat/cg-cat-20150130.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="r2cat and treecat, scaffolding tools for ordering and orienting contigs"
+HOMEPAGE="http://bibiserv.techfak.uni-bielefeld.de/cgcat"
+SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/cgcat/resources/downloads/r2cat.tar.gz"
+# SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/cgcat/resources/downloads/r2cat.jar"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=">=virtual/jre-1.6:*"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/r2cat
+
+src_prepare(){
+	sed -e "s#/vol/bioapps#"${D}"/usr#" -e "s#/vol/bibidev/r2cat#"${D}"/usr#" -i Makefile
+}
+
+src_compile(){
+	emake
+}
+
+src_install(){
+	# emake install dies with:
+	# jarsigner -tsa https://timestamp.geotrust.com/tsa -keystore /homes/phuseman/.gnupg/jarsigner_keystore_cg-cat  cg-cat.jar cgcat
+	# Enter Passphrase for keystore: jarsigner: you must enter key password
+	# Makefile:44: recipe for target 'cg-cat.jar' failed
+	mkdir -p "${D}"/usr/share/r2cat
+	emake install_cebitec
+	emake install_bibiserv
+}
+
+# java -Xmx1024M -jar r2cat.jar
+# java -Xmx1024M -cp r2cat.jar de.bielefeld.uni.cebitec.treecat.Treecat -Xmx -d64

diff --git a/sci-biology/cg-cat/metadata.xml b/sci-biology/cg-cat/metadata.xml
new file mode 100644
index 0000000..1699e58
--- /dev/null
+++ b/sci-biology/cg-cat/metadata.xml
@@ -0,0 +1,12 @@
+<?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>

[gentoo-commits] proj/sci:master commit in: sci-biology/cg-cat/

[Martin Mokrejs]

commit:     3dfc64c1f97b791372ed2bfd1e7c2b7e297dedf7
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 14 10:37:07 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 14 10:37:07 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3dfc64c1

sci-biology/cg-cat: working ebuild, still could provide shellscript callers to call the java .jar file and add -d64 on amd64 hosts

Package-Manager: portage-2.2.26

 sci-biology/cg-cat/cg-cat-20150130.ebuild | 35 +++++++++++++++++++++++--------
 1 file changed, 26 insertions(+), 9 deletions(-)

diff --git a/sci-biology/cg-cat/cg-cat-20150130.ebuild b/sci-biology/cg-cat/cg-cat-20150130.ebuild
index af9a76a..af5e731 100644
--- a/sci-biology/cg-cat/cg-cat-20150130.ebuild
+++ b/sci-biology/cg-cat/cg-cat-20150130.ebuild
@@ -13,20 +13,26 @@ SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/cgcat/resources/d
 
 LICENSE="GPL-3"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
 IUSE=""
 
-DEPEND=">=virtual/jre-1.6:*"
-RDEPEND="${DEPEND}"
+RDEPEND="${DEPEND}
+	>=virtual/jre-1.6:*
+	dev-lang/perl
+	sci-biology/ncbi-tools"
+DEPEND="${RDEPEND}
+	>=virtual/jdk-1.6:*
+	dev-java/ant-core"
 
 S="${WORKDIR}"/r2cat
 
 src_prepare(){
-	sed -e "s#/vol/bioapps#"${D}"/usr#" -e "s#/vol/bibidev/r2cat#"${D}"/usr#" -i Makefile
+	sed -e "s#/vol/bioapps#"${D}"/usr#" -e "s#/vol/bibidev/r2cat#"${D}"/usr#" -i Makefile || die
+	sed -e "s#/vol/gnu#/usr#" -i de/bielefeld/uni/cebitec/r2cat/blast_to_r2cat.pl || die
 }
 
 src_compile(){
-	emake
+	emake r2cat.jar
 }
 
 src_install(){
@@ -35,9 +41,20 @@ src_install(){
 	# Enter Passphrase for keystore: jarsigner: you must enter key password
 	# Makefile:44: recipe for target 'cg-cat.jar' failed
 	mkdir -p "${D}"/usr/share/r2cat
-	emake install_cebitec
-	emake install_bibiserv
+	# emake install_cebitec
+	# emake install_bibiserv
+	# the blast_to_r2cat.pl script needs bioperl
+	dobin de/bielefeld/uni/cebitec/r2cat/blast_to_r2cat.pl
+	java-pkg_dojar r2cat.jar || die
+	dodoc README.md ReadmeLicenses.txt
+	insinto /usr/share/doc/"${PN}"/html
+	doins de/bielefeld/uni/cebitec/r2cat/help/*
 }
 
-# java -Xmx1024M -jar r2cat.jar
-# java -Xmx1024M -cp r2cat.jar de.bielefeld.uni.cebitec.treecat.Treecat -Xmx -d64
+# to start r2cat:
+# java -Xmx10240M -jar r2cat.jar de.bielefeld.uni.cebitec.r2cat.R2cat
+
+# to start treecat:
+# java -Xmx10240M -cp r2cat.jar de.bielefeld.uni.cebitec.treecat.Treecat -Xmx -d64
+
+# add -d64 on the java commandline if you need more than 4GB of memory and your system can handle it

[gentoo-commits] proj/sci:master commit in: sci-biology/cg-cat/

[Andrew Ammerlaan]

commit:     9131388e7578eca5d5bb1ae1aa069ffa0cbc83ad
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 10:17:45 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 10:17:45 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9131388e

sci-biology/cg-cat: EAPI bump

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/cg-cat/cg-cat-20150130.ebuild | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/sci-biology/cg-cat/cg-cat-20150130.ebuild b/sci-biology/cg-cat/cg-cat-20150130.ebuild
index b83ebd996..0c48ecbc5 100644
--- a/sci-biology/cg-cat/cg-cat-20150130.ebuild
+++ b/sci-biology/cg-cat/cg-cat-20150130.ebuild
@@ -1,7 +1,7 @@
-# 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
 
 inherit java-pkg-2 java-ant-2
 
@@ -13,7 +13,6 @@ SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/cgcat/resources/d
 LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~amd64"
-IUSE=""
 
 RDEPEND="${DEPEND}
 	>=virtual/jre-1.6:*
@@ -26,6 +25,7 @@ DEPEND="${RDEPEND}
 S="${WORKDIR}"/r2cat
 
 src_prepare(){
+	default
 	sed -e "s#/vol/bioapps#"${D}"/usr#" -e "s#/vol/bibidev/r2cat#"${D}"/usr#" -i Makefile || die
 	sed -e "s#/vol/gnu#/usr#" -i de/bielefeld/uni/cebitec/r2cat/blast_to_r2cat.pl || die
 }
@@ -46,8 +46,8 @@ src_install(){
 	dobin de/bielefeld/uni/cebitec/r2cat/blast_to_r2cat.pl
 	java-pkg_dojar r2cat.jar || die
 	dodoc README.md ReadmeLicenses.txt
-	insinto /usr/share/doc/"${PN}"/html
-	doins de/bielefeld/uni/cebitec/r2cat/help/*
+	docinto html
+	dodoc de/bielefeld/uni/cebitec/r2cat/help/*
 }
 
 # to start r2cat: