Hello,

I have been using Gorilla gene ontology with help from a great post on BioStars Automating Gorilla And/Or Revigo Analysis

However, a colleague wishes to use 8 separate analyses listed on http://software.broadinstitute.org/gsea/msigdb/index.jsp for each comparison in our project

I have a lot of analyses to run (19 gene lists * 8 gene sets = 152 runs) that I'm supposed to run through their pipeline, and needless to say, doing this manually through a browser can be very error-prone, which is why I want to do this on the command line like was done on the previous link.

I've asked this question on https://groups.google.com/forum/#!topic/gsea-help/ltnk_y1JSdY and he said that this sort of analysis isn't possible on their site, but if it has survived this long, there has to be a way to automate this for large analyses. The Gorilla site manager also said that it isn't possible, but wasn't aware of Automating Gorilla And/Or Revigo Analysis I'm hoping that the same holds true for MSigDB

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/

is there some way I can automate this, as was done with the gorilla data set?