Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. ... written in Java. ---- CYTOSCAPE LICENSE AGREEMENT ---- GNU LESSER GENERAL PUBLIC LICENSE Version 2.1, February 1999 http://www.cytoscape.org/download.php?file=cyto2_5_2 http://www.cytoscape.org/
Created attachment 159916 [details] cytoscape-2.6.0.ebuild Here's the first stab at an ebuild. This package has a ton of bundled jars, which we'll need to get rid of before this can go into mainline.
Created attachment 159986 [details] cytoscape-2.6.0.ebuild Lots of fixes to the ebuild. Removed most jars that are in the tree. Added blockers on request bugs for freehep and biojava. Unfortunately this will now pull in a HUGE list of dependencies.
One thing that I've noticed is that the Cytoscape core plugins are bundled with the binary releases of Cytoscape, but don't seem to be in the source tarball. Without the core plugin jars, the application as compiled from the source tarball is an empty shell. The core plugins are not in the plugin directory on the website, either.
Created attachment 160002 [details] cytoscape-2.6.0.ebuild Ah, never mind. My bad, I had set the plugins path wrong in src_install.
(In reply to comment #4) > Created an attachment (id=160002) [edit] > cytoscape-2.6.0.ebuild > > Ah, never mind. My bad, I had set the plugins path wrong in src_install. > EANT_ANT_TASKS="jakarta-regexp-1.4 batik-1.6 xalan xsdlib relaxng-datatype" Sorry if I misinformed you, but don't add all the runtime dependencies to EANT_ANT_TASKS just the ones that's needed by an ant task. (batik for example)
Serkan- Those are not runtime dependencies. Those correspond to the jars I found in the build-libs subdirectory. I haven't checked yet which of them correspond to actual build tasks.
Created attachment 160460 [details] cytoscape-2.6.0.ebuild More deps cleanup, shortcut icon. See blocker bugs for some of the remaining deps.
The package is now available in the java-experimental overlay: http://overlays.gentoo.org/proj/java/browser/java-experimental/sci-biology/cytoscape This overlay is not in layman, so it must be checked out manually using svn co https://overlays.gentoo.org/svn/proj/java/java-experimental and adding to PORTDIR_OVERLAY in make.conf.
# emerge -pv cytoscape * Overlay eclasses override eclasses from PORTDIR: * * '/usr/local/java-experimental/eclass/java-pkg-2.eclass' * '/usr/local/java-experimental/eclass/java-utils-2.eclass' * '/usr/local/java-experimental/eclass/mercurial.eclass' * * It is best to avoid overriding eclasses from PORTDIR because it will * trigger invalidation of cached ebuild metadata that is distributed with * the portage tree. If you must override eclasses from PORTDIR then you * are advised to add FEATURES="metadata-transfer" to /etc/make.conf and to * run `emerge --regen` after each time that you run `emerge --sync`. Set * PORTAGE_ECLASS_WARNING_ENABLE="0" in /etc/make.conf if you would like to * disable this warning. These are the packages that would be merged, in order: emerge: there are no ebuilds to satisfy "dev-java/piccolo2d". (dependency required by "sci-biology/cytoscape-2.6.1" [ebuild]) (dependency required by "cytoscape" [argument])
Martin- piccolo2d is in the java overlay. Add it with layman -a java-overlay. (You'll need to follow layman setup instructions if you haven't used layman before) Sorry I forgot to mention that.
>>> Emerging (1 of 1) sci-biology/cytoscape-2.6.1 from java-experimental * WizardSource.jar RMD160 SHA1 SHA256 size ;-) ... [ ok ] * cytoscapeSource-v2.6.1.tar.gz RMD160 SHA1 SHA256 size ;-) ... [ ok ] * checking ebuild checksums ;-) ... [ ok ] * checking auxfile checksums ;-) ... [ ok ] * checking miscfile checksums ;-) ... [ ok ] * Using: sun-jdk-1.6 >>> Unpacking source... >>> Unpacking WizardSource.jar to /var/tmp/portage/sci-biology/cytoscape-2.6.1/work >>> Unpacking cytoscapeSource-v2.6.1.tar.gz to /var/tmp/portage/sci-biology/cytoscape-2.6.1/work * Removing bundled jars... ./lib/build-libs/batik-css.jar ./lib/build-libs/batik-dom.jar ./lib/build-libs/batik-ext.jar ./lib/build-libs/batik-rasterizerTask.jar ./lib/build-libs/batik-util.jar ./lib/build-libs/batik-awt-util.jar ./lib/build-libs/batik-script.jar ./lib/build-libs/batik-parser.jar ./lib/build-libs/batik-svg-dom.jar ./lib/build-libs/batik-bridge.jar ./lib/build-libs/batik-transcoder.jar ./lib/build-libs/batik-gvt.jar ./lib/build-libs/batik-xml.jar ./lib/build-libs/batik-rasterizer.jar ./lib/build-libs/jakarta-regexp-1.4.jar ./lib/build-libs/xalan.jar ./lib/build-libs/xsdlib.jar ./lib/build-libs/relaxngDatatype.jar ./lib/swing-layout-1.0.1.jar ./lib/swingx-2006_10_27.jar [cut] >>> Source unpacked in /var/tmp/portage/sci-biology/cytoscape-2.6.1/work >>> Compiling source in /var/tmp/portage/sci-biology/cytoscape-2.6.1/work ... Rewriting attributes Rewriting ./docs/build.xml Rewriting ./wizard/build.xml Rewriting ./build.xml * Using following ANT_TASKS: jakarta-regexp-1.4 batik-1.7 xalan xsdlib relaxng-datatype jaxb-2 jaxb-tools-2 !!! ERROR: Package swingx was not found! * * ERROR: sci-biology/cytoscape-2.6.1 failed. * Call stack: * ebuild.sh, line 48: Called src_compile * environment, line 4133: Called java-pkg-2_src_compile * environment, line 2248: Called eant 'jar' '-f' 'build.xml' * environment, line 911: Called java-pkg_getjars 'swing-layout-1,stax-ex,xmlstreambuffer,sjsxp,concurrent-util,jsr173,jsr181,jsr250,saaj-api,fastinfoset,itext,jdom-1.0,junit,colt,javahelp,jgoodies-looks-2.0,swingx,l2fprod-common,tclib,piccolo2d,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,jaxb-2,jaxb-tools-2,batik-1.7' * environment, line 2916: Called die * The specific snippet of code: * [[ $? != 0 ]] && die "java-config --classpath=${pkgs} failed"; * The die message: * java-config --classpath=swing-layout-1,stax-ex,xmlstreambuffer,sjsxp,concurrent-util,jsr173,jsr181,jsr250,saaj-api,fastinfoset,itext,jdom-1.0,junit,colt,javahelp,jgoodies-looks-2.0,swingx,l2fprod-common,tclib,piccolo2d,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,jaxb-2,jaxb-tools-2,batik-1.7 failed * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/tmp/portage/sci-biology/cytoscape-2.6.1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/cytoscape-2.6.1/temp/environment'. * This ebuild is from an overlay named 'java-experimental': '/usr/local/java-experimental/' * !!! When you file a bug report, please include the following information: GENTOO_VM=sun-jdk-1.6 CLASSPATH="" JAVA_HOME="/opt/sun-jdk-1.6.0.12" JAVACFLAGS="-source 1.6 -target 1.6" COMPILER="javac" and of course, the output of emerge --info !!! ERROR: Package jaxb-tools-2 was not found! !!! ERROR: Package jaxb-tools-2 was not found! Buildfile: build.xml It seems having swingx-0.9.5 is not helpful. I will probably have to downgrade to the 2007 version once I find the sources (bug #161710).
# svn diff sci-biology/cytoscape/cytoscape-2.6.1.ebuild Index: sci-biology/cytoscape/cytoscape-2.6.1.ebuild =================================================================== --- sci-biology/cytoscape/cytoscape-2.6.1.ebuild (revision 7705) +++ sci-biology/cytoscape/cytoscape-2.6.1.ebuild (working copy) @@ -20,7 +20,7 @@ LICENSE="LGPL-2.1" SLOT="0" IUSE="" -KEYWORDS="~amd64" +KEYWORDS="~amd64 ~x86" COMMON_DEPS="dev-java/swing-layout:1 dev-java/stax-ex @@ -39,7 +39,7 @@ java-virtuals/jsr224 dev-java/javahelp dev-java/jgoodies-looks - =dev-java/swingx-20070211-r1 + dev-java/swingx >=dev-java/l2fprod-common-7.3-r1 dev-java/tclib dev-java/piccolo2d Should depend also on bug #188007
Created attachment 253663 [details] cytoscape-2.8.0_beta2.ebuild Version bump; this distribution is just jars, so complete ebuild is not possible. However, the number, variety, and version-specificity of bundled jars make un-bundling seem like a bad idea to me, as generally-useful packages like biojava can't go to the most-recent version.
Feel free to reopen if you're still interested in adding this ebuild to the Portage tree. Closing as WONTFIX.
Cytoscape is a flagship project and it is missing in Gentoo.
Fair enough. Removing java@ from CC in this case. As far as we are concerned, we have no interest in maintaining/packaging sci libs.
An ebuild for cytoscape (binary) is in the Guru overlay: https://gitweb.gentoo.org/repo/proj/guru.git/tree/sci-biology/cytoscape-bin
