Many of the queue submission scripts use dumb relative paths which assume invocation from the pipeline folder. Eg. `sgerun_MKTRUTH.sh` assumes it can call `bin/alignmentToTruth.py` regardless of working dir.
Many of the queue submission scripts use dumb relative paths which assume invocation from the pipeline folder.
Eg.
sgerun_MKTRUTH.shassumes it can callbin/alignmentToTruth.pyregardless of working dir.