working version

orca_wrap.sh

@@ -202,8 +202,8 @@ do
         shift
 done
 
-_positional_names=('_arg_inputdir')
-for (( ii = 0; ii < 2; ii++)); do
+_positional_names=('_arg_inputdir' )
+for (( ii = 0; ii < 1; ii++)); do
    eval "${_positional_names[ii]}=\${_positionals[ii]}" || die "Error during argument parsing, possibly an Argbash bug." 1
 done
 
@@ -241,37 +241,33 @@ if [ -z "$SLURM_JOB_ID" ]; then
        ### check if output directory already exists
        if [[ ! -d "${_arg_outdir// }"  ]]; then
            _arg_outdir="$(pwd)/${_arg_tag}"
-           mkdir -p "${_arg_outdir}"
+           mkdir -p "${_arg_outdir/%j/}"
        else
            error "${_arg_outdir// } exists already! Possibly over overwrite of results. Cowardly giving up."
        fi
 
        sbatch -A "${_arg_assoc}" -p parallel -J "${_arg_tag}" -o "${_arg_outdir}" -n 40 -t 120:00:00 --signal=B:SIGUSR2@600 -N 1 --wrap "$(cat << EOF
+       set -x
        cleanup(){
          cp /localscratch/${SLURM_JOB_ID}/* "\${_arg_outdir}"
        }
        trap 'cleanup' SIGUSR2
-       cp $sample /localscratch/\${SLURM_JOB_ID}
+       scratch=/localscratch/\${SLURM_JOB_ID}
+       cp $sample "\$scratch"
        # Go to jobdir and start the program
        cd /localscratch/\${SLURM_JOB_ID}
        set OMPI_MCA_btl=self,sm
-       orca $sample
+       eval $(which orca) "\$scratch"/$(basename $sample)
        cleanup
 EOF
 )"
    done
 fi
 
-
-https://stackoverflow.com/questions/53071681/use-of-a-heredoc-with-slurm-sbatch-wrap
-
-
-EOF
-)
        #./orca.sh ${sample}
-       done
-   fi
+#       done
+#   fi
 
 
-https://stackoverflow.com/questions/53071681/use-of-a-heredoc-with-slurm-sbatch-wrap
+#https://stackoverflow.com/questions/53071681/use-of-a-heredoc-with-slurm-sbatch-wrap