Mutational Signatures: create a Docker image for this, and push to Dockerhub

[evanbiederstedt]

No description provided.

[kpjonsson]

From this: https://github.com/mskcc/mutation-signatures

Should be run on the final somatic MAF file.

[kpjonsson]

To be specific:

python make_trinuc_maf.py input.maf input.trinuc.maf && \
python main.py Stratton_signatures30.txt input.trinuc.maf input.mutsig.txt

[evanbiederstedt]

@hweej nailed it, give the guy a raise people

https://hub.docker.com/r/cmopipeline/mutation-signatures

[evanbiederstedt]

In psuedo-code, here’s what it does is:

1. check to see if the maf inputted has the string ‘trinuc’ in it. If not, run the trinuc command on the maf and save the path to the outputted file
2. run the “mutational signatures script” (main.py) on the maf with trinuc information (edited)
   The first command is:
   python make_trinuc_maf.py 'path/to/maf' 'path/to/output/maf/withTrinuc'
   The output is:
   'path/to/output/maf/withTrinuc'
   The second command is python main.py 'path/to/Stratton_signatures30.txt' 'path/to/maf/annotated/withTrinuc' 'path/to/output'
   I suggest we ignore the --spectrum and --spectrum_output

EDIT: MAFs output from the pipeline always need to be processed through python make_trinuc_maf.py

[kpjonsson]

More precisely, the make_trinuc_maf.py script adds the column Ref_Tri to the MAF and that is the column the main.py script uses.

[evanbiederstedt]

More precisely, the make_trinuc_maf.py script adds the column Ref_Tri to the MAF and that is the column the main.py script uses.

Right! I should also clarify that the MAFs output from the pipeline always need to be processed through python make_trinuc_maf.py