msconvert 1.3

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# msconvert-py

A python wrapper for the [pwiz/msconvert docker image](https://hub.docker.com/r/proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses).

# Why?

In my personal experience running the docker container directly may cause some problems:

• On large machines the containers eat up a lot of memory because the garbage collection rarely kicks in.

• Memory seems to leak when rescoring multiple files in one msconvert run.

• Limiting the memory usage is difficult because conversion may require somewhere between ~3G and ~30G.

• The conversion is single threaded.

# How to run

Install the package via pip install msconvert and run it via python -m msconvert.

By default, the module will convert every *.raw file in the current directory to .mgf. However, there are other options available:

• -i Input path (default is current directory)

• –input-format Input format (default raw)

• –output-format Output format (default mgf)

• –concurrency Concurrency (default is number of cores)

# How it works

• Msconvert-py runs each conversion in a dedicated docker container.

• Each container is initially limited to 3G memory.

• When a container fails due to an out-of-memory kill it will be re-run with +8G memory.

• The containers run concurrent, per default up to the number of cores.

• Containers are only started as soon as there is memory available as defined to the memory limit.