One of the main routes to mzML-formatted data is using Open Source converter msconvert. It can convert to mzML from most of the vendor formats. In PhenoMeNal, we have now succeeded to package msconvert in a Docker container and execute it in the WINE environment (“Run Windows applications on Linux, BSD, Solaris and Mac OS X”). And wait, there is more! We can even demonstrate that it is possible to integrate this into the Galaxy workflow system, again running on a Linux server.
The Dockerfile build script is hosted as part of the PhenoMeNal github team in the docker-pwiz repository. Of course, nothing is perfect (yet). For example, WINE currently crashes with some of the vendor formats, but their developer version has improved in this area a lot. Or, currently the Galaxy integration is only a technology demonstration, where the docker container is invoked locally.
The real power comes in when the Galaxy dockerized tools can execute anywhere, ranging from local workstations to in-house OpenStack clusters but also on public cloud providers such as Google cloud. In PhenoMeNal we also aim at massively parallelizing conversion and, thus, speeding up the computationally intensive and time demanding process of conversion. Stay tuned, seamless MS data conversion is coming to a workflow near you!
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Author: Steffen Neumann