Hi!

Yeah, the pipeline documentation is not ready yet. There are also going to be more tweaks on the Cistrome pipeline. It would be great if you will also participate in the pipeline testing

I recommend you to work on the latest snapshot instead of 1.12.1, it is even more updated: http://ugene.unipro.ru/snapshot.html

Some info about how to configure Cistrome and the data, required for it, can be found here: http://ugene.unipro.ru/ugene_niaid.html
However the docs here are a little obsolete. For example, there is no more need in installing the python tools (django and others) - they should be inside the "embedded python" external tool.

Regards,
Olga