Difficultly Importing Gene Panel Files in Docker Deployment

[Matthew West]

Hi there,

I was hoping someone would be able to help with importing a gene panel for a cBioPortal  docker deployment.

At the moment, I have the following workflow:

• In one terminal window, cd to cbioportal-docker-compose, run docker compose up. This runs successfully and hangs on 
        INFO: Starting ProtocolHandler ["http-nio-8080"]
  (which I think is expected behaviour). Instance is running at http://localhost:8080/.
• In another terminal window, I run the following command in order to import my gene panel. I have more than one, so I am assuming I need to run this multiple times:

docker-compose run \
    -v /Users/matthew.west/cbioportal-docker-compose/study/my_gene_panels/gene_panels/data_gene_panel_rs.txt:/gene_panels/gene_panel.txt:ro \
    cbioportal
    bash -c 'cd /cbioportal/core/src/main/scripts/ && ./importGenePanel.pl --data /gene_panels/gene_panel.txt'

This is based on the documentation provided here. I have only edited the path following the -v flag, up to the first colon, and nothing else (it is not clear to me based on the precedent set in other docs whether or not I need to edit the paths in the bash command).

When I run this command, output is generated, but it hangs on INFO: Starting ProtocolHandler ["http-nio-8080"], just like in the 'main' terminal window, in which I ran docker compose up. In that terminal window, there is also the following output, though not sure if this is root of our problem as I have seen it elsewhere:

'@'172.18.0.6' (using password: YES)   | 2023-08-31T13:51:59.490945Z 6 [Note] Access denied for user 'cbio_user

 

Is this behaviour expected and how can we troubleshoot? Is the the gene panel command supposed to exit, and if not, how do you handle importing multiple gene panel files? (earlier processes are killed when I try and run 4+ gene panel windows in parallel). Happy to provide more detailed logs in the event that those would be useful.

Kind regards,

Matthew West

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[Matthew West]

Hi there,

I think I found the source of the issue! The command I'm running does not have a backslash after 'cbioportal'.

Since I copied and pasted this from your documentation website, I would recommend updating your docs accordingly.

Thank you for everything you do!

Kind regards,

Matthew West

[de Bruijn, Ino]

Hi Matthew,

 

Thanks so much for sharing your solution! Apologies for not getting back to you sooner. Updated the docs:

 

https://github.com/cBioPortal/cbioportal/commit/d6ce4a4c8669b205fc26aa03e737f28c86e9868d

 

Should be live on the docs site in a few minutes. Let us know if notice any other issues

 

Thanks so much!

Ino

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