Package Details: cytoscape 3.7.1-1

Git Clone URL: https://aur.archlinux.org/cytoscape.git (read-only, click to copy)
Package Base: cytoscape
Description: A software for visualizing molecular interaction networks and integration with gene expression profiles and other state data.
Upstream URL: http://www.cytoscape.org
Licenses: LGPL2
Submitter: timdiels
Maintainer: lukaszimmermann
Last Packager: lukaszimmermann
Votes: 11
Popularity: 0.000007
First Submitted: 2015-09-22 13:00
Last Updated: 2019-03-19 15:06

Dependencies (2)

Required by (0)

Sources (4)

Latest Comments

interrupthandler commented on 2020-12-05 11:28

Current version bump to 3.8.2

I was playing with the PKGBUILD and updated it to version 3.8.2 by making the following changes

  1. Changed pkgver
  2. Updated the URL to match the new release naming scheme as of 3.8.2
  3. Computed the sha256sum for the updated package and added it to the PKGBUILD

I have included a gist with the illustrated changes for your convenience. I'd be delighted to help co-maintain and test the package long term.

https://gist.github.com/evikv/cb2191582103e939bb3c78d8554144e5

essenceoffoo commented on 2020-07-13 08:48

FYI: I installed Cytoscape 3.8. with the official Linux installer from cytoscape.org. Java 8-openjdk did not work, but Java 11-openjdk does. I haven't tried Java 14-openjdk.

khughitt commented on 2020-02-06 23:45

One more suggestion -- Cytoscape is not compatible with recent versions of Java so you first have to install an earlier version (JDK-8 is the one currently listed as supported), and then you should be able to launch cytoscape with "JAVA_HOME=/usr/lib/jvm/java-8-openjdk cytoscape"

balwierz commented on 2019-07-10 16:11

Crash at startup

Error occurred during initialization of boot layer java.lang.module.FindException: Module java.transaction not found

alienzj commented on 2019-03-18 13:57

https://github.com/cytoscape/cytoscape/releases/download/3.7.1/cytoscape-3.7.1.tar.gz

alienzj commented on 2019-03-18 13:57

outdate

timdiels commented on 2017-06-20 08:33

If you anyone still gets "JAVA_HOME not set", set it in your shell's login script (~/.bash_profile, /etc/profile.d):
export JAVA_HOME=/usr/lib/jvm/default

pwl commented on 2016-11-02 13:36

It doesn't work, I'm getting:

$ cytoscape
karaf: JAVA_HOME not set; results may vary
Exception in thread "main" java.lang.UnsupportedClassVersionError: org/cytoscape/launcher/internal/Launcher : Unsupported major.minor version 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:803)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)