Cytoscape 3.1.0

[osmar]

Hi there, I have recently formatted my pc and I am trying to download Cytoscape core files again. I found that svn files are on 3.1.0 version while git's version is 3.0.0. I have followed the git tutorial and the launching freezes while loading prefuse modules. Can someone help me on this?

Thanks,

Osmar Cavalcante.

[Peng-Liang Wang]

Hi Osmar,

Cytosape repository has been moved to gitHub since Cytoscape 3.0. You should look at the Cytosape code in git hub

https://github.com/cytoscape/cytoscape

Can you be more specific about what the problem you run into?

Thanks,

Peng

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[Jason Montojo]

Hi Osmar,

Which version of Cytoscape do you need?  The latest development happens on the Git "develop" branch, which is version 3.1.0-SNAPSHOT.  The latest stable release is on the "master" branch, which is 3.0.0.  Our next service release is 3.0.1 which is on the "hotfix/3.0.1" branch.

Are you getting any error messages in the console when you launch?

Thanks,

Jason

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[osmar]

I have cloned the project using the repo scripts and installed with mvn clean install, as instructed by the tutorial. The splash screen freezes on loading layout-prefuse-impl and a lot of bundles loading errors appear on my console. When I was using 3.1.0 version the system was running smoothly.

ex. Cytoscape 3.0.0> ERROR: Bundle org.cytoscape.application-impl [129] Error starting mvn:org.cytoscape/application-impl/3.0.0 (org.osgi.framework.BundleEx

ception: Activator start error in bundle org.cytoscape.application-impl [129].)

[Jason Montojo]

Hi Osmar,

Sounds like you have a caching issue.  Can you try deleting the directory CytoscapeConfiguration/3/karaf_data (in your home directory) and try running Cytoscape again?

Thanks,

Jason

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[osmar]

I have already tried this, with no sucess. Same errors. ;\

[Peng-Liang Wang]

I think the version in branch hotfix/3.01 is better tested than the one in the develop branch. You may try 'git checkout hotfix/3.01' and then 'mvn clean install'.

Peng

[Jason Montojo]

Hi Osmar,

Based on your log output, it looks like your Maven repository has a mixture of 3.0.0 bundles and 3.1.0-SNAPSHOT bundles.  There are a few ways to fix this.  The easiest is to do a full rebuild of the whole thing.  You can do that by running "mvn clean install" in your top-level clone (i.e. the directory that contains api, impl, gui-distribution).  Next, you should run Cytoscape using the launch scripts in gui-distribution/assembly/target/cytoscape.

Hope this helps,

Jason