Issue with BRAKER and AUGUSTUS
I can't make BRAKER1 working, because of a bad "design" in AUGUSTUS (in my opiniion).
In simple, I had pushed my BRAKER1 job to pass the GeneMark part. But it couldn't continue with augustus, because when augustus knows I am annotating a new species, it would try to write the AUGUSTUS installation directory for the parameter files.
I have AUGUSTUS installed in a distributed system, and since a few people will use it, I installed it system wide, meaning everyone can use "module load" method to call AUGUSTUS, but only the "root" or system adim (when sudo-ed as root) can write inthe installation directory.
So I can't make AUGUSTUS to run.
I am wondering whether you could really make the use of the "workingdir" option? Could you have the parameter files for a new species to be written in the "workingdir"? This seems easy, since you just need to change "AUGUSTUS_CONFIG_PATH" in script new_species.pl to "workingdir", and reference to workingdir ever since.