Question

[AlexandrMiroshnikov]

Hello. I want to use your guide on Read the Book site. There are any changes in PIP since 2016? If I'll go scenario, don't I meet any troubles because of upgrades?
I saw that some scripts uses your cluster. How can I do that tutorial on my local machine? It's possible, to copy modules, that your script require?

[kalekundert]

I'll try to answer your specific questions below, but the big-picture answer is that this software has never been used outside of UCSF, and getting it to work elsewhere will probably run into all sorts of problems. I'm happy to provide guidance, but I don't have the bandwidth to generalize the code myself.

There have been a number of changes made since 2016, but not many since 2018. See the commit log for details. The documentation should still be reasonably up-to-date, though.

You should be able to run the tutorial scripts on your local machine, because they don't actually use PIP or the cluster. They just run the same rosetta commands that PIP would run, but with many fewer replicates.