centralised, consistent definition of HOMER installation

fmicompbio / monaLisa

binned motif enrichment analysis and visualisation

https://fmicompbio.github.io/monaLisa/

GNU General Public License v3.0

34 stars 5 forks source link

centralised, consistent definition of HOMER installation #22

Closed mbstadler closed 3 years ago

mbstadler commented 5 years ago

Currently, there are several functions that need to call different scripts or binaries from HOMER:

findHomer: search for file in path
prepareHomer: prepare a binned motif enrichment analysis
runHomer: run a binned motif enrichment analysis
clusterPWMs: similarities between PWMs
runHomerDenovo: does not exist yet

Maybe it would be worth thinking about how the path to HOMER scripts/binaries could be configured or defined in a consistent and maybe shared way across these.

mbstadler commented 3 years ago

This may become obsolete as we are on the way to become independent of HOMER

mbstadler commented 3 years ago

As we do not exclusively depend on HOMER anymore, this is currently not worth the effort.