Why is lsaBGC-Pan failing at the OrthoFinder stage?
This is likely because of the way OrthoFinder 2 (we haven't switched to v3 yet) gets installed via Bioconda and how the lsaBGC-Pan's conda env bin/ folder might not appear as first up in the $PATH env variable for users after activation. The solution is pretty simple, after activating simply update and run:
export PATH=$CONDA_PREFIX/bin:$PATH
If this does not resolve the issue when you rerun lsaBGC-Pan, please just let us know on GitHub issues.
Why is lsaBGC-Pan failing when using Panaroo?
The is likely because we do not include Panaroo in the lsaBGC-Pan Bioconda recipe and it has to be manually installed in the lsaBGC-Pan environment.
This is likely because of the way OrthoFinder 2 (we haven't switched to v3 yet) gets installed via Bioconda and how the lsaBGC-Pan's conda env
bin/folder might not appear as first up in the$PATHenv variable for users after activation. The solution is pretty simple, after activating simply update and run:If this does not resolve the issue when you rerun lsaBGC-Pan, please just let us know on GitHub issues.
The is likely because we do not include Panaroo in the lsaBGC-Pan Bioconda recipe and it has to be manually installed in the lsaBGC-Pan environment.