Proteomic Pipeline generator is a command line script that generates multiple pipelines for use with proteomics data.
The PPG currently uses two types of software: database search software, and statistical validation software. It also offers statistical enrichment analysis with g:profiler and pathway analysis with Reactome.
- PeptideProphet (not avalible outside of the TPP)
- Percolator
- Tandem2XML (not avalible outside of the TPP)
- idconvert
- tandem2pin & msgf2pin
Add the location of the programs that you have installed to second collumn of the install_locations file.
If no programs are added the script will check PATH for installation.
The PPG is issued with multiple variables some are required.
Options required to generate the pipelines
-P [Programs to build pipelines for]
Options required to automaticaly run the pipelines
-i [input file(s)]
-p [parameterfiles] (in the same order as the programs)
Optional variables
-l [logfile location]
-o [output directory]
-L [Directory where the scripts will be generated]
-s [options] (for use on the LUMC sharkcluster calls the scripts with qsub with everyting after the -s)
the -s option has to be added at the end of the command line
example: -s -pe BWA 4 -cwd
-n || --norun causes the scripts to not run
-g || --genparam only generates the parameter files
--autorun automaticaly run the pipeline when running localy.
-S || --noScripts Don't generate new scripts you can give the location of the scripts you want to run after the -S.
-f creates one script for each database search program with all the statistical validators.
--autorun won't ask you if you want to run locally
-h Display this file
-r [incrementing value] [start point] [end point] the start point has to be greater than 0 and the incrementing value can only have one decimal value