Open juliadouglasf opened 2 months ago
best_by_compleasm.py calls compleasm.py . It has a command line argument --compleasm_bin that needs to hand over the compleasm.py file. If your compleasm is hidden in an environment that is not activitated while BRAKER is running, then BRAKER cannot see compleasm.py, and can thus not determine the $COMPLEASM_PATH variable that points to the location of compleasm.py .
I have compleasm in the same environment as BRAKER, so I don't think I will have the issue of compleasm not being found while BRAKER is running. The compleasm
command seems to be working the same as compleasm.py
.
Hello,
I have been running BRAKER using a conda environment coupled with GeneMark and ProtHint git installations. I know this is not the recommended method, but it is simpler, especially if I incorporate it into a Snakemake pipeline later on in my work.
I received a
$COMPLEASM_PATH not set!
error even though bothcompleasm
andbest_by_compleasm.py
are included in my conda environment bin path. I think BRAKER is checking forcompleasm.py
, which doesn't seem to exist. With my conda environment activated,compleasm --help
works as expected. Since I believe BRAKER only uses thebest_by_compleasm.py
script, I don't think this$COMPLEASM_PATH not set!
error should be thrown and stop my execution of BRAKER.