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kellrott / SMC-Het-Challenge-Eval

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run on ctpsingle #5

Open galder-max opened 5 years ago

galder-max commented 5 years ago

From salem:

Dockerfile: _" FROM smalikic/dreamchallenge_base_image RUN git clone https://smalikic@bitbucket.org/smalikic/docker_ctpsingle_pcawg.git RUN cp -rf docker_ctpsinglepcawg/* /opt/CTPsingle/ " And following email: _"Dear Maxime,

I had a look at differences between CTPsingle submissions for PanCancer and DREAM Challenge. (i) When comparing the two versions, they require exactly the same set of R libraries etc. so the same docker base images can be used. (ii) I created new bitbucket repo and stored there version of CTPsingle used in PCAWG (iii) Now The only file that needs to be changed is "Dockerfile" (changing reference of source code = bitbucket repo link). I have attached that file here - is it possible that you take it from here and use it, or it requires some additional (upload) steps to be completed by myself?

Thank you very much for the help.

PS If file can not be opened, below is its content (3 lines):

FROM smalikic/dreamchallenge_base_image RUN git clone https://smalikic@bitbucket.org/smalikic/docker_ctpsingle_pcawg.git RUN cp -rf docker_ctpsingle_pcawg/* /opt/CTPsingle/

Salem"_

kellrott commented 5 years ago

Are there Galaxy tool XML wrappers for this tool? I don't see one in https://bitbucket.org/smalikic/docker_ctpsingle_pcawg/src

galder-max commented 5 years ago

Salem is checking that it runs on his side and will come back to us.

galder-max commented 5 years ago

Just sent another reminder.

galder-max commented 5 years ago

@kellrott question from Salem: "Can you please give me any advice how can I test and verify that docker actually works well? Because the one I initially made was for SMC-Het and it was working well and later you contacted me reporting some issues (as I can remember in SMC-Het I could test online whether the tool works)"

i guess we dont have the credit/setup to test the galaxy dockers anymore. if there is a docker ready, is the easiest to test on your end?

smalikic commented 5 years ago

Are there Galaxy tool XML wrappers for this tool? I don't see one in https://bitbucket.org/smalikic/docker_ctpsingle_pcawg/src

I have some XML files in

https://bitbucket.org/smalikic/docker_ctpsingle_pcawg/src/master/scriptsForPreparingDocker/myScriptsDREAMchallenge/

Would they work?

galder-max commented 5 years ago

@kellrott Could you have a look at the docker scripts from salem?

@smalikic Are these from your previous submission or the new one?