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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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--config-IonQuant flag #894

Closed avera1988 closed 1 year ago

avera1988 commented 1 year ago

Hi,

I am trying to run fragpipe in a headless mode in our HPC. I was dealing to configure the location of IonQuant, I had to start a GUI session and there save the configuration of the paths pointing to philosopher, MS-Fragger and IonQuant. I noticed that users can specify the paths for both Philospher and ms-fragger using the flags --config-msfragger and --config-philosopher . However, I am wondering if there is a flag for also specifying the path to IonQuant without the necessity to run the GUI. For some other clusters, GUI is not possible to run.

Thanks!

Arturo.

fcyu commented 1 year ago

Duplicated issue: https://github.com/Nesvilab/FragPipe/issues/733