Cytoscape broken on linux

bioconda / bioconda-recipes

Conda recipes for the bioconda channel.

https://bioconda.github.io

MIT License

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Cytoscape broken on linux #30692

Open izahn opened 2 years ago

izahn commented 2 years ago

Cytoscape currently does not work for me on linux:

$ mamba create -n cstest -c bioconda cytoscape
<SNIP>
$ conda activate cstest
$ cytoscape.sh
karaf: JAVA_HOME not set; results may vary
Error occurred during initialization of boot layer
java.lang.module.FindException: Module javafx.web not found

I have a working build in https://github.com/conda-forge/staged-recipes/pull/16131 but I have been advised to coordinate with the bioconda community.

dpryan79 commented 2 years ago

Conda-forge is a dependency of bioconda, for whatever it's worth. I'm guessing from the error that there are some java version issues with the current recipe. Can you make a PR on bioconda just copying over your PR on staged-recipes? The files should go in recipes/cytoscape.

izahn commented 2 years ago

Ah, makes sense. I will prepare a PR for recipes/cytoscape.