sebastian-luna-valero
commented
3 years ago Hi,
I agree. However, before making the change, I see that we install macs2=2.1.1.20160309:
https://github.com/cgat-developers/cgat-flow/blob/master/conda/environments/pipelines-macs2.yml#L10
which seems to be available for Python 2.7 only. If we want to install macs2 for Python 3 it will have to be a later version > 2.2.2:
https://anaconda.org/bioconda/macs2/files
Is it worth checking that a newer version of macs2 won't break existing pipelines?
For example:
- https://github.com/cgat-developers/cgat-flow/blob/master/cgatpipelines/tasks/intervals.py#L1099
- https://github.com/cgat-developers/cgat-flow/blob/master/cgatpipelines/tasks/peakcalling.py#L732
- https://github.com/cgat-developers/cgat-flow/blob/master/cgatpipelines/tasks/peakcalling.py#L1317
Best regards, Sebastian
CGATflow installation creates a separate, python2, environment for MACS. But the latest versions of MACS2 are now python3 compatible. Installing the python2 version means that we are both getting an out of date version of MACS and creating extra installation headaches.