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Diffstat (limited to 'sci-biology/cg-cat/cg-cat-20150130.ebuild')
| -rw-r--r-- | sci-biology/cg-cat/cg-cat-20150130.ebuild | 59 |
1 files changed, 0 insertions, 59 deletions
diff --git a/sci-biology/cg-cat/cg-cat-20150130.ebuild b/sci-biology/cg-cat/cg-cat-20150130.ebuild deleted file mode 100644 index 0c48ecbc5..000000000 --- a/sci-biology/cg-cat/cg-cat-20150130.ebuild +++ /dev/null @@ -1,59 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -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="~amd64" - -RDEPEND="${DEPEND} - >=virtual/jre-1.6:* - dev-lang/perl - sci-biology/ncbi-tools" -DEPEND="${RDEPEND} - >=virtual/jdk-1.6:* - dev-java/ant-core" - -S="${WORKDIR}"/r2cat - -src_prepare(){ - default - sed -e "s#/vol/bioapps#"${D}"/usr#" -e "s#/vol/bibidev/r2cat#"${D}"/usr#" -i Makefile || die - sed -e "s#/vol/gnu#/usr#" -i de/bielefeld/uni/cebitec/r2cat/blast_to_r2cat.pl || die -} - -src_compile(){ - emake r2cat.jar -} - -src_install(){ - # emake install dies with: - # jarsigner -tsa https://timestamp.geotrust.com/tsa -keystore /homes/phuseman/.gnupg/jarsigner_keystore_cg-cat cg-cat.jar cgcat - # Enter Passphrase for keystore: jarsigner: you must enter key password - # Makefile:44: recipe for target 'cg-cat.jar' failed - mkdir -p "${D}"/usr/share/r2cat - # emake install_cebitec - # emake install_bibiserv - # 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 - docinto html - dodoc de/bielefeld/uni/cebitec/r2cat/help/* -} - -# 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 |