running GSEA from command line

[David Condon]

Hello,

I am attempting to run GSEA via the command line.  I cannot see how to do this based on the documentation http://software.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html?_Other_Ways_to and http://software.broadinstitute.org/gsea/doc/GSEAUserGuideTEXT.htm#_Running_GSEA_from_the%20Command%20Line

I just want to specify

1. species as "human",
2. "gene list" where "gene_list" is a file,
3. for each analysis listed on http://software.broadinstitute.org/gsea/msigdb/

I don't see how I can specify these three items on the command line.

How can I do these?

-Dave

[David Eby]

Hi Dave,

The analyses listed on that web page are completely different from the GSEA Desktop software.  Those analyses are meant as a more light-weight manner of investigating the gene sets in MSigDB for web users; we don't provide any means for running them at the command line.

Regards,

David

David Eby
Consultant
Cancer Informatics Development
Broad Institute of MIT and Harvard
415 Main St, Cambridge, MA 02142, USA
http://www.broadinstitute.org/cancer
http://www.gsea-msigdb.org
https://twitter.com/GSEA_MSigDB
https://twitter.com/GenePattern

[David Condon]

hi Dave,

I have 152 separate analyses that need to be done.  Is there any way I could automate this at all?

thanks,
-Dave

[David Eby]

Do you mean automating use of the web tools like Compute Overlaps?  We don't have any support for that.

I'm pretty sure there are users out there writing command-line scripts to query our tools (maybe using 'curl' or 'wget') but it's not something we've ever investigated or supported ourselves so there's nothing more I can say about it.

If you mean automating GSEA Desktop analyses, yes, that is possible.  See our User Guide for more information.

David Eby
Consultant
Cancer Informatics Development
Broad Institute of MIT and Harvard
415 Main St, Cambridge, MA 02142, USA
http://www.broadinstitute.org/cancer
http://www.gsea-msigdb.org
https://twitter.com/GSEA_MSigDB
https://twitter.com/GenePattern