Need execulable errors to exit scripts about stir-gate-connection HOT 4 CLOSED

easy thing is to use set -e at the start. It does make the script stop whenever there's an error (that isn't inside a pipeline, etc). It does exit abruptly though without any message. We can switch it to bash and then do something like this
https://github.com/UCL/STIR/blob/7b4c27470ad175a80f29e9aabe945b6831a4f159/scripts/estimate_scatter.sh#L104-L105

set -e # exit on error
trap "echo ERROR in $0" ERR

Obviously better is to do

if apply_normfactors3D $OutputFilename $factors ones.hs 1 1 $eff_iters
then
  : #OK
else
  echo "Error over here" >2;exit 1
fi

but it's much more verbose. In nearly all Bourne shells implementations you can shorten this to

if ! apply_normfactors3D $OutputFilename $factors ones.hs 1 1 $eff_iters
then
  echo "Error over here" >2;exit 1
fi

but apparently it isn't 100% portable 😢 (although I cannot immediately find a link to that info anymore)

from stir-gate-connection.

Is there anything wrong with

apply_normfactors3D $OutputFilename $factors ones.hs 1 1 $eff_iters
if [ $? -eq 0 ]; then
    echo "apply_normfactors3D OK"
else
    echo "apply_normfactors3D FAIL"
    exit 1
fi

besides it being verbose?

e: The first option seems to work nicely.

from stir-gate-connection.

sure, that's fine and even more verbose 😄

from stir-gate-connection.

Resolved with 3fef6c4

from stir-gate-connection.