Modify handling of JobOptions that specify executables
There are a few jobtypes, relion.autopick.topaz
variants and relion.localres.resmap
where there is a JobOption for specifying where an executable is. This is a holdover from Relion but it makes these jobs different from all others in the pipeliner where executables need to be in the path.
To bring these in line with everything else in the pipeliner these executables should be in the job's self.jobinfo.programs
and the job marked unavailable if they are not in the PATH.
The JobOptions
should be left in place for Relion compatibility, but they can be added to the hidden Relion JobOptions
and autofilled with the path using shutil.which()