Collection of material including data files, scripts, workflows and results for the proteomics use cases described in the publication "Automated workflow composition from a pool of bioinformatics tools: a demonstration for mass spectrometry data analysis" (in preparation).

The workflows of the four use cases are easily executed within the given Docker container. However, the bash scripts can also be adapted to run independently by adjusting the paths of the used software tools (if available on the respective computer).

Download files
git clone https://github.com/veitveit/Automatic-Workflow-Composition

Create docker image:
docker -t workflow-composition .
This will take a while.
(you need to be in the folder Automatic-Workflow-Composition)

Run workflows
E.g. Use case 3 workflow 1:
docker run -it workflow-composition
cd UseCases/Use_case_3-PTM_identification/Workflow1
bash FullPipeline
You can also run the R scripts with R CMD BATCH GivenRScriptName and/or extract the files with docker cp