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cgat-developers / cgat-flow

cgat-flow repository
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R functionality in cgatflow #121

Closed jscaber closed 3 years ago

jscaber commented 4 years ago

Supersedes previous email - I have created an "issue" instead

I have tried to merge the experiment.R functionality with the existing cgatflow pipeline. I realised this may be better placed elsewhere, but as this is the most experimental repository that fewest people use, I thought placing the functionality here would be best.

cgatflow.py main now looks for the arguments "cgatflow R" and if these are present does argument parsing which ultimately leads to command line tools in a new "Rtools" subdirectory.

This would allow calling "cgatflow R tool" from the pipeline itself.

Realise this might be a little hacky so open to other suggestions.

Please review commit 9c7f06a

Acribbs commented 4 years ago

Hi @jscaber

Its looking good so far,do you want me to help with anything?

jscaber commented 3 years ago

Hi @Acribbs

not sure if you're still interested in this, but for my own benefit have been rewriting the rnaseqdiffexpression pipeline for a while. The R scripts have been ready for some time, but have started working on the pipeline, getting rid of rpy2 and of the unwieldy counts2table and also experiment.py.

After discussion with both Andreas and David, I have gone for a setup involving direct calling of R scripts rather than altering cgatflow.py.

Don't need help but if you want to input or comment, you're welcome to join and happy to talk also. It's likely that you already have a working setup elsewhere

Branch is #JS-rnaseqdiffexpression.py

Acribbs commented 3 years ago

Very keen!

Will take a look tomorrow. Thanks.