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lazear / sage

Proteomics search & quantification so fast that it feels like magic
https://sage-docs.vercel.app
MIT License
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Specifying Temporary Directory #50

Closed kostrouc closed 1 year ago

kostrouc commented 1 year ago

Is there an option to specify a temporary directory for sage? I don't see it in the --help. It also does not appear to be integrated with SearchCLI? Not sure if I am running these commands correctly, but I cannot process a very large mzML file without the use of a temporary directory.

Below is what I have tried using the conda installation of SearchCLI: searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI -id_params myparameters.par -db myproteins.fasta -spectrum_files "/mnt/data/large.mzML" -sage_folder ./sage -sage 1 -search_engine_temp /mnt/data/temp/

I have also tried with the sage binary, but -temp_folder does not appear to be a command and I don't see anything listed for it in the example json. ./sage myparameters.json -temp_folder /mnt/data/temp/

lazear commented 1 year ago

Can you clarify what you mean by "cannot process a very large mzML file without the use of a temporary directory."?

Sage has no concept of a temporary directory, and one shouldn't be needed - everything is done in RAM. Can you run the sage binary on the mzML file like ./sage myparameters.json /mnt/data/large.mzML?