qSVA preparatory code doesn't work in Docker

sidbdri / cookiecutter-de_analysis_skeleton

Skeleton for new differential expression analysis project.

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qSVA preparatory code doesn't work in Docker #139

Closed lweasel closed 3 years ago

lweasel commented 3 years ago

Because the region_matrix.py code (which is very old) doesn't work in Python 3.

hxin commented 3 years ago

The qSVA we are using is from here, it only supports python 2.x

I guess we can either:

swap to an R equivalent, not sure how this will work out I just did a few searches and found this (see ref)
or change nothing but call python2 specifically when doing qSAVE, i.e python2 /opt/region_matrix/./region_matrix.py

This is just to confirm that python2 works in the VE in docker (I used the docker container that you created just now for the FLTD project to test it out, hence it's your username)

I prefer the latter though...

hxin commented 3 years ago

The latter also does not require any change in docker, as we can hardcode the python2 in the run_analysis.sh script instead.

lweasel commented 3 years ago

Yeah, hardcding python2 is probably easiest, isn't it. That's what I just did in the current container to get it to work.

hxin commented 3 years ago

Okay i will create a fix later today

On Fri, 15 Jan 2021 at 14:37, Owen Dando notifications@github.com wrote:

Yeah, hardcding python2 is probably easiest, isn't it. That's what I just did in the current container to get it to work.

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hxin commented 3 years ago

I can't find the qsva code in the dev branch which was in master here. Anyone can point me where it is? @lweasel @katieemelianova

lweasel commented 3 years ago

May need to re-add it again, in snakemake style.