Process to use non-standard organism index unclear

[j-andrews7]

Following genescape build, it doesn't seem like providing the resulting index to genescape web does anything. "Human" and "Mouse" are still available in the dropdown, the index stats are the same on "Draw Tree" click - utils.index_stats index: 288,575 mappings, 19,606 symbols, 18,680 terms, and plugging in symbols from the custom index results in no hits.

I may simply be doing something wrong, but a more clear example of how this can be done would be helpful.

[ialbert]

The documentation now notes how users need to invoke the tool to pass an index to it

 genescape tree --index myindex.gz genelist.txt