Raw files are readable and searchable via Docker container using this simple trick

[avcarr2]

I am in a situation where I don't really want to convert .raw to .mzml and then upload to the cloud to search. I noticed that the RawFileReader repo over on Thermo's GitHub also says that it is compatible with Linux. The error that I get on Linux when attempting searches with .raw files is related to the interactive prompt in MetaMorpheus. Fortunately, there's a workaround to this. You just need to pipe in the expected response, in this case echo "y" is piped to docker container running in interactive mode (-i flag). To use the example from the wiki, the command to run MM would look like:

echo "y" | docker run -i --rm -v /Users/user/MetaMorpheusVignette:/vignette smithchemwisc/metamorpheus:1.0.5 -t vignette/Task1-SearchTaskconfig.toml vignette/Task2-CalibrateTaskconfig.toml vignette/Task3-SearchTaskconfig.toml vignette/Task4-GPTMDTaskconfig.toml vignette/Task5-SearchTaskconfig.toml -s {Directory with Raw Files} -d vignette/uniprot-mouse-reviewed-1-24-2018.xml.gz vignette/uniprot-cRAP-1-24-2018.xml.gz

[avcarr2]

I'm also working on a pull request to add a command line argument to just accept the Thermo terms and conditions.