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bgruening / docker-galaxy-exome-seq

Galaxy Docker Image for Exome sequencing
MIT License
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MIRACUM Workflow compatibility #16

Closed DanielAmsel closed 5 years ago

DanielAmsel commented 5 years ago

Dear *, after a chat with @wm75 , I would like to share my / our experiences within this issue.

I encountered several problems when I tried to run the MIRACUM workflow on this container. Maybe one could address the problems within this repo or create an own MIRACUM workflow fork?

Just for the sake of completeness, I would like to say that the Galaxy version could be updated to the current one.

More urgently, the following tools are missing in the build to run the workflow properly:

Tools that had to be re-installed:

I also ran into troubles because the Workflow uses once hg19 references and elsewhere hg19full. Downloading the genome worked for me, but not indexing with bwa. So @wm75 gave me the hint, to start the container with --priviledged.

Best regards, Daniel

wm75 commented 5 years ago

Thanks for listing all problems in such detail! This will definitely help me to update the docker image here, but also the MIRACUM workflow using it.

wm75 commented 5 years ago

Tools that had to be re-installed:

  • [ ] fastqc 0.72

This is most likely related to https://github.com/galaxyproject/tools-iuc/pull/2406 and should be fixed automatically once the image gets rebuilt.

DanielAmsel commented 5 years ago

Tools that had to be re-installed:

  • [ ] fastqc 0.72

This is most likely related to galaxyproject/tools-iuc#2406 and should be fixed automatically once the image gets rebuilt.

Ok even better. I just documented what I did, to have it running ;)

Thank you again @wm75 for all the support and the --priviledged advice!

bgruening commented 5 years ago

I triggered a rebuild. Hope that will fix it. Have a nice weekend!

wm75 commented 5 years ago

All above issues with the image should be fixed in the latest version. Please open new issues for remaining bugs.