Msgf not working on AWS! - Githubissues

nf-core / quantms

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

https://nf-co.re/quantms

MIT License

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Msgf not working on AWS! #25

Closed jpfeuffer closed 2 years ago

jpfeuffer commented 2 years ago

1nxf-scratch-dir ip-172-31-26-118.eu-west-1.compute.internal:/tmp/nxf.XXXXSM8v5U

Input file 'MSGFPlus.jar' could not be found (by searching on PATH). Either provide a full filepath or fix your PATH environment!

Error: File not found (the file 'MSGFPlus.jar

jpfeuffer commented 2 years ago

What ever it is, it probably also applies to Luciphor which is also a jar

ypriverol commented 2 years ago

Are you using the docker in AWS?

jpfeuffer commented 2 years ago

Yes it is using docker. But AWS does not set workflow.containerengine

Anyway, it needs to be tested and working for all configurations.