search

CoBrALab / qbatch

The Unlicense
27 stars 13 forks source link

Environment can break --help #177

Closed bcdarwin closed 5 years ago

bcdarwin commented 5 years ago 
$ qbatch --help
qbatch: error: QBATCH_SYSTEM set to slurm but sbatch not found

seems similar to https://github.com/Mouse-Imaging-Centre/pydpiper/issues/147 ... :)

pipitone commented 5 years ago

Jumping in on this issue. My suggestion here is to refactor so that _setupVars() does not force an exit if the required binaries for the queuing system aren't found. Instead, this check should be a preflight check only, right before jobs are launched at the bottom of qbatchDriver()

gdevenyi commented 5 years ago

@pipitone agree, that's exactly where the problem lies :+1: