readw-dockerized

This is a dockerized version of ReAdW for use in the Cravatt lab. This allows us to convert .RAW files collected from Thermo mass spectrometers to .mzXMLs for downstream analysis. ReAdW was designed for use in Windows but this project makes it available on Linux through the use of Docker and wine.

Use

docker run --rm -v path_to_raw_files:/raw -v $PWD/output:/output radusuciu/readw-dockerized /raw/experiment_123

The last argument above can be a folder containing .raw files, or it can be a .raw file itself. You may specify multiple .raw files, or folders by just adding more arguments. Matching for the .raw extension is case insensitive as some machines output .RAW files by default.

Output files will be placed in the output directory of your choice. You can change the second mount above to that effect.

Installation Requirements

Docker is required to build and run this image. Additionally, the following .dll files must be obtained from a licensed install of Xcalibur:

• fileio.dll
• fregistry.dll
• XRawfile2.dll
• zlib1.dll

These must be placed in the readw folder. After that you can simply docker build . to build the image.

Useful Links:

• https://github.com/PedrioliLab/docker-readw
• https://github.com/PedrioliLab/ReAdW
• http://proteomicsresource.washington.edu/protocols06/wine/