Package Details: cytoscape 3.8.2-1

Git Clone URL: https://aur.archlinux.org/cytoscape.git (read-only, click to copy)
Package Base: cytoscape
Description: Network Data Integration, Analysis, and Visualization in a Box
Upstream URL: http://www.cytoscape.org
Licenses: LGPL
Submitter: timdiels
Maintainer: a821
Last Packager: a821
Votes: 11
Popularity: 0.000003
First Submitted: 2015-09-22 13:00
Last Updated: 2021-03-02 09:39

Required by (0)

Sources (4)

Latest Comments

Keystone commented on 2021-02-16 16:05

JAVA_HOME out of the box not being set is annoying, but not having AA enabled makes this software nearly impossible to use.

The application command entry might benefit from being changed to reflect one or both improvements:

1 Depend on jdk8 and link it directly + turn on AA:

JAVA_HOME=/usr/lib/jvm/java-8-openjdk/ _JAVA_OPTIONS='-Dawt.useSystemAAFontSettings=on' cytoscape

2 Don't depend on jdk8 and turn on AA:

_JAVA_OPTIONS='-Dawt.useSystemAAFontSettings=on' cytoscape

I used #1 while working towards getting this running.

K

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)