PORTAL_HOME in docker deployment

[Peter Saffrey]

Hi there,

 

I’ve deployed a copy of cBioPortal using the docker-based instructions here:

 

https://docs.cbioportal.org/deployment/docker/

 

Now I’m trying to accession my own data using the `metaImport.py` script, based on instructions here:

 

https://docs.cbioportal.org/using-the-metaimport-script/

 

Running the script gives an error about missing jar files:

 

                Expected to find 1 scripts-*.jar, but found 0

 

And reading the docs in more detail it looks like I need to define a PORTAL_HOME that will point to some jar files created during compilation. Except because I deployed with docker, I didn’t compile anything. Where can I find these jar files? Or do I need to run the import script from inside the docker environment?

 

Thanks,

 

Peter

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[Luke Sikina]

Hi Peter,

The PORTAL_HOME variable is already defined in the docker container. My guess is that your import command just needs some tweaking. This is what I use to import the UCSF study:

    docker-compose exec cbioportal metaImport.py -u http://cbioportal:8080 -s study/lgg_ucsf_2014/ -o

Hope that helps!

- Luke

[Peter Saffrey]

Hi Luke,

Thanks for your reply. I actually found this in the meantime by looking more closely at the documentation.

It might be worth adding a link from the accessioning docs:

https://docs.cbioportal.org/using-the-metaimport-script/

To the specific section that deals with using this script in a local/docker install:

https://docs.cbioportal.org/deployment/docker/import_data/#step-2---import-data

Thanks,

Peter