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Enable easy deployment of tpp search library creation and swath workflows on windows and linux.
- create
- tpp search workflow up to protein prophet (15.01.2015)
- library creation workflow - builds on search workflow (22.01.2015)
SearchCake -> python package
searchWF.py - (WW) libraryCreateWF.py - (LB)
SearchCake_Binaries (windows and linux binaries) - (WW) SearchCake_Data (testdata) - (WW)
SwathCake - (LB)
swathWF.py - (LB)
SwathCake_Binaries (windows and linux binaries) -> python package (LB)
- openswathworkflow.exe
- pyprophet
- msproteomicstools (feature aligner requant)
SwathCake_Data (WW i.e. 5 files from Gold standard, mzXML)
conversion pipeline - msconvert - qtofpeakpicker - swath windows update
MSConvertCake -> python package MSConvertCake_Data -> DDA sample, SWATH gold standard wiffs (WW). MSConvertCake_Binaries -> python package (WW/LB)
python packages for workflow and binaries -> git repo fors data
specify / find binaries?
- executable in path
- executable from package
Python package has class which returns path to exectuble either from path variable or if not in path to the executable shipped with package
Set path to exectuble into ini file Write ini file into working directory Start Workflow
- location specified in ini file
Do not change ini
How to call the workflow:
In working directory there is an input.ini file for workflow.
searchWF.py --INPUT input.ini --OUTPUT output.ini --TPP /usr/bin/tpp/
- find out how to pass input ini location to ruffus
- additional parameters mit command line
- ruffus workflows as apps - is this possible
pyporophet.py --INPUT input.ini --MPR_NUM_XVAL 35