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
