try using HOMER with conda

[sreichl]

HOMER still gets installed "manually" via a rule.
This occasionally leads to hard to find/understand problems in peak_calling step.
Maybe it's time to try to make it work for conda.

https://anaconda.org/bioconda/homer
https://bioconda.github.io/recipes/homer/README.html
https://github.com/bioconda/bioconda-recipes/tree/master/recipes/homer

[fwzhao]

One very helpful intermediate step would be to copy/redirect the stdout stderr of peak_calling shell script to a log that is kept. Currently, when peak_calling fails, the respective "fail" logs for each individual step are lost, and it becomes difficult to debug.

Before this issue is closed, I'd suggest a fresh install of HOMER (delete previous path) if anyone has issues that don't make sense. In my case, it was of an outdated HomerConfig.pm file, that existed but couldn't be read somehow by Homer - "Can't locate HomerConfig.pm in... "

And the only thing that fixed it was a complete reinstall (not just perl configureHomer.pl in pre-existing Homer path)

[sreichl]

yes, good point. should redirect all log to {log} directive but without messing with the multiQC setup.