diff options
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/cytoscape/cytoscape-2.7.0.ebuild | 144 |
1 files changed, 144 insertions, 0 deletions
diff --git a/sci-biology/cytoscape/cytoscape-2.7.0.ebuild b/sci-biology/cytoscape/cytoscape-2.7.0.ebuild new file mode 100644 index 0000000..8f77943 --- /dev/null +++ b/sci-biology/cytoscape/cytoscape-2.7.0.ebuild @@ -0,0 +1,144 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI="2" + +EANT_ANT_TASKS="jakarta-regexp-1.4 batik-1.7 xalan xsdlib relaxng-datatype jaxb-2" +EANT_GENTOO_CLASSPATH="swing-layout-1,stax-ex,xmlstreambuffer,sjsxp,concurrent-util,jsr173,jsr181,jsr250,saaj-api,fastinfoset,junit,batik-1.7,freehep-graphicsio-svg,freehep-util,freehep-xml,freehep-export,freehep-graphicsio,freehep-graphicsio-java,freehep-swing,freehep-graphicsio-ps,freehep-io,freehep-graphics2d,freehep-misc-deps,itext,swingx-0.9,piccolo2d,tclib" +JAVA_ANT_REWRITE_CLASSPATH="true" + +inherit versionator java-pkg-2 java-ant-2 eutils + +MY_PV=$(replace_all_version_separators '_') + +DESCRIPTION="A visualization platform for molecular interaction networks" +HOMEPAGE="http://www.cytoscape.org/" +SRC_URI="http://chianti.ucsd.edu/Cyto-${MY_PV}/cytoscapeSource-v${PV}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +COMMON_DEPS="dev-java/swing-layout:1 + dev-java/stax-ex + dev-java/xmlstreambuffer + dev-java/sjsxp + dev-java/concurrent-util + dev-java/jsr173 + dev-java/jsr181 + dev-java/jsr250 + java-virtuals/saaj-api + dev-java/fastinfoset + dev-java/itext + dev-java/jdom:1.0 + dev-java/junit + dev-java/colt + dev-java/javahelp + >=dev-java/swingx-0.9.5 + >=dev-java/l2fprod-common-7.3-r1 + dev-java/tclib + dev-java/piccolo2d + ~dev-java/biojava-1.6 + dev-java/freehep-graphicsio-java + dev-java/freehep-graphicsio-ps + dev-java/freehep-graphicsio-svg + dev-java/freehep-xml + dev-java/jgoodies-looks:2.0" +# dev-java/jaxb dev-java/javahelp +DEPEND=">=virtual/jdk-1.6 + dev-java/jakarta-regexp:1.4 + >=dev-java/batik-1.7-r1 + dev-java/xalan + dev-java/xsdlib + dev-java/relaxng-datatype + ${COMMON_DEPS}" +RDEPEND=">=virtual/jre-1.6 + ${COMMON_DEPS}" + +S="${WORKDIR}" + +java_prepare() { + einfo "Removing bundled jars..." + find -name 'stax-ex.jar' -print -delete + find -name 'saaj.jar' -print -delete + find -name 'streambuffer.jar' -print -delete + find -name 'sjsxp.jar' -print -delete + find -name 'concurrent.jar' -print -delete + find -name 'jsr*.jar' -print -delete + find -name 'FastInfoset.jar' -print -delete + find -name 'jaxws-*.jar' -print -delete + find -name 'http.jar' -print -delete + find -name 'activation.jar' -print -delete + find -name 'glf.jar' -print -delete + find -name 'freehep*.jar' -print -delete + find -name 'itext*.jar' -print -delete + find -name 'swingx*.jar' -print -delete + find -name 'piccolo*.jar' -print -delete + find -name 'jnlp.jar' -print -delete +# find -name 'wizard.jar' -print -delete +# find -name 'jaxb*.jar' -print -delete +# find -name 'swingunit.jar' -print -delete + + cd extra-jars + find -name '*.jar' -print -delete + cd "${S}" + + cd lib + find -name 'colt.jar' -print -delete + java-pkg_jar-from colt + find -name 'jhall.jar' -print -delete + java-pkg_jar-from javahelp + find -name 'looks-*.jar' -print -delete + java-pkg_jar-from jgoodies-looks-2.0 + find -name 'jdom*.jar' -print -delete + java-pkg_jar-from jdom-1.0 + find -name 'junit.jar' -print -delete + java-pkg_jar-from junit + find -name 'l2fprod-common*.jar' -print -delete + java-pkg_jar-from l2fprod-common + find -name 'swing-layout*.jar' -print -delete + java-pkg_jar-from swing-layout-1 + find -name 'biojava*.jar' -print -delete + java-pkg_jar-from biojava + find -name 'tclib.jar' -print -delete + cd "${S}" + + cd lib/build-libs + find -name 'batik*.jar' -print -delete + java-pkg_jar-from batik-1.7 + find -name 'jakarta*.jar' -print -delete + java-pkg_jar-from jakarta-regexp-1.4 + find -name 'xalan*.jar' -print -delete + java-pkg_jar-from xalan + find -name 'xsdlib*.jar' -print -delete + java-pkg_jar-from xsdlib + find -name 'relaxngDatatype.jar' -print -delete + java-pkg_jar-from relaxng-datatype + cd "${S}" + + # Skip the jalopy ant build target (produces access violations) + perl -i -ne 'print unless /taskdef.*name="jalopy"/../<\/target>/' build.xml || die + + # TODO: HACK. Rip out the rasterize task because of batik incompatibility + perl -i -ne 'print unless /taskdef.*name="rasterize"/../<\/taskdef>/' build.xml || die + perl -i -ne 'print unless /^\s*<rasterize/../^\s*dest=.*>/' build.xml || die +} + +src_install() { + java-pkg_dojar cytoscape.jar + java-pkg_dojar lib/*.jar + java-pkg_jarinto /usr/share/${PN}/plugins + java-pkg_dojar plugins/core/*.jar + + # replacement for resources/bin/cytoscape.sh + java-pkg_dolauncher cytoscape.sh --main cytoscape.CyMain \ + --java_args '-Dswing.aatext=true -Xss5M -Xmx512M' \ + --pkg_args '-p '/usr/share/${PN}/plugins' \"$@\"' + insinto /usr/share/pixmaps + newins images/icon100.png cytoscape.png + make_desktop_entry cytoscape.sh Cytoscape /usr/share/pixmaps/cytoscape.png + + dodoc docs/pdf/manual.pdf +} |