Yes, the best guide is in the manual that is included with the pathway-tools installation.

Thanks.
I have another question if you don’t mind.
Do you know what do this PathwayTools flags do:
-disable-metadata-saving
-nologfile

And are there a guide with all the command of PathwayTools? Do you know?

Yes you can, see the last command in this post.

Jeff,
Thanks for the detailed answer! I’ll read through the publication’s M&M, which admittedly I haven’t done yet.
Cheers,
Brandon

Brandon,
No links, and the format of the files are simply those specified by the pathway-tools module pathologic. To make this easier I’ve built the method into the paprica pipeline that I’ve been working on. Use the paprica-mg_build.py and paprica-mg_run.py scripts available from the development version of paprica on Github. Note that this requires you to build the paprica database first, which takes some dependencies and time. If you don’t want to do that you can deconstruct the paprica-mg.py script, but I’d recommend building the database. Be aware that at this time there is a bug in pathway-tools that prevents PGDBs being built in parallel. I think the pathway-tools people are working on this and hopefully there will be a fix out very soon. Until this is fixed it takes a very long time to build the paprica database.

Hope sounds interesting to you! greetings.