Deseq2 error in Galaxy

Question: Deseq2 error in Galaxy

8 months ago by

Hi,

I am running a docker container with Galaxy in it. The container was provided by a 3rd party, on which I installed DeSeq2. DeSeq2 returns an error message:

/export/galaxy-central/database/job_working_directory/000/40/tool_script.sh: line 9: R: command not found /export/galaxy-central/database/job_working_directory/000/40/tool_script.sh: line 9: Rscript: command not found

Can you please suggest how I can fix it? Thanks!

dependencies conda rna-seq docker deseq2 • 432 views

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modified 8 months ago by ylebras • 20 • written 8 months ago by ivanovaos.09 • 0

How did you installed DESeq2? Can you check which version of Galaxy is installed in this container? http://localhost:8080/api/version for example should tell you, assuming localhost:8080 is were your container is running.

ADD REPLY • link written 8 months ago by Bjoern Gruening ♦ 5.1k

I have been provided with the folder with ready-to-use DESeq2 and I installed it manually (copied to the tools/ folder in the galaxy-central, and then added it to the config file - tool_conf.xml).

<section id="deseq" name="deseq_2" >
<tool file="deseq2/deseq2.xml" />   </section>

It was used by someone else beforehand, with the same set-up and it worked fine. Here is what api/version address returned:

{"extra": {}, "version_major": "17.05"}

ADD REPLY • link modified 8 months ago • written 8 months ago by ivanovaos.09 • 0

8 months ago by

ylebras • 20

ylebras • 20 wrote:

Hi ivanovaos,

Can you give us more information about how you have installed Deseq2 ? Have you used the main ToolShed repo https://toolshed.g2.bx.psu.edu/view/iuc/deseq2/d983d19fbbab ? Your Galaxy instance is based on the bgruening galaxy-stable Docker image https://github.com/bgruening/docker-galaxy-stable ? I guess you are admin, so you can look at the Admin/Manage Tool Dependencies/ page and see what is indicated for the DeSeq2 tool ? And maybe try to check the related box and use the "Install checked dependencies using Conda" button to resolve the issue who seems to be related to the fact that no dependencies are found by Galaxy...

Cheers,

Yvan

ADD COMMENT • link written 8 months ago by ylebras • 20

Dear Yvan,

Thank you very much for your reply. I have no information if the image used was stable, unfortunately, but I assume it is stable. I am indeed an admin and when I am trying to install dependencies using the way you described, the page is just updated without any error messages, but the dependencies are marked with the red sign (still not installed/resolved). I tried to restart Galaxy to check if the dependencies will be updated, but it didn't help. :(

Here is what api/version address returned:

{"extra": {}, "version_major": "17.05"}

Cheers, Olga

ADD REPLY • link modified 8 months ago • written 8 months ago by ivanovaos.09 • 0

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