Proteowizard msconvert Docker Buildfile
The first step in a metabolomics data processing workflow with Open Source tools is the conversion to an open raw data format like [mzML]:https://github.com/HUPO-PSI/mzML/ .
One of the main routes to mzML-formatted data is using Open Source converter msconvert developed by the Proteowizard team (Chambers et al. 2012), which is one of the reference implementations for mzML. It can convert to mzML from Sciex, Bruker, Thermo, Agilent, Shimadzu, Waters and also the earlier file formats like mzData or mzXML.
Although Proteowizard was initially targeting LC/MS data, it can also readily convert GC/MS data for example from the Waters GCT Premier or Agilent instruments.
Building the Docker image
Please note that for licensing reasons we can not include all required files in this repository. Please head over to http://proteowizard.sourceforge.net/downloads.shtml and place the installer pwiz-setup-3.0.9098-x86.msi in this directory. Also note that the build is known to fail with Docker-1.9, make sure to use Docker-1.10 or above.
docker build --tag="phnmnl/pwiz:latest" .
Using the Docker image
After building the image, the conversion can be started with e.g.
docker run -v $PWD:/data:rw phnmnl/pwiz:latest /data/neg-MM8_1-A,1_01_376.d -o /data/ --mzML
The currently tested vendor formats are:
- mzXML:
docker run -it -v $PWD:/data phnmnl/pwiz:3.0.9098-0.1 threonine_i2_e35_pH_tree.mzXML - Bruker *.d:
docker run -it -v $PWD:/data phnmnl/pwiz:3.0.9098-0.1 neg-MM8_1-A,1_01_376.d
Galaxy usage
A rudimentary Galaxy node description is included as msconvert.xml,
it was obtained from the msconvert.ctd using
python CTD2Galaxy/generator.py -i /vol/phenomenal/vmis/docker-pwiz/msconvert.ctd -m sample_files/macros.xml -o /vol/phenomenal/vmis/docker-pwiz/msconvert.xml