tumordeconv/prot-data repository overview

⁠Proteomics Module

This module enables the collection of proteomics patient data using the cptac Python package to collect mRNA data for one of six available cancer types. This module includes the following:

⁠To run

There are three ways to get proteomics data, depending on your environment. Each one should output a file.tsv in your local directory

⁠If you have Python and cptac installed

Simply run the command

python getAllDatasets.py
python protDataSetsCLI.py --cancerType=brca

⁠If you have Docker installed

Then you can run the command via the docker interactive mode

docker build . -t prot-module
docker run --volume $PWD:/tmp -ti prot-module python /bin/protDataSetsCLI.py --cancerType=brca

⁠If you have Docker and a CWL engine

Here we have an example using the cwl-tool engine, but this should run any other engine as well.

cwl-tool prot-data-cwl-tool.cwl --cancerType brca

If using alongside another CWL implementation (like toil-cwl-runner or arvados-cwl-runner), you can install then run with cwltool:

pip install cwltool
cwltool prot-data-cwl-tool.cwl --cancerType brca

⁠Cancer types