i try run docker with entrypoint.sh, but it doesn't exequite .sh line:
echo `ls -d /input/sub-*/ | sed -e 's/.*sub-\(.*\)\//\1/' | split -l 8 - participants_`
I wrote it in dockerfile:
ENTRYPOINT ["bash", "-c", "source /code/entrypoint.sh | ts '[%Y-%m-%d %H:%M:%S]' &>> /output/stderr.log"]
Why echo doesn't execute inside docker run [my_image]
Here is full entrypoint.sh code:
#! /bin/bash
alias time='/usr/bin/time -f "%C --- CPU:\t%E real,\t%U user,\t%S
sys\t%P\tMem:\t%KkiB avg.,\t%MkiB max.\tExit:\t%x"'
echo `ls -d /input/sub-*/ | sed -e 's/.*sub-\(.*\)\//\1/' | split -l 8 -
participants_`
while read input_bids_path
do
participants_id=$(basename $input_bids_path)
LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH
time fmriprep /input /output participant --fs-license-file
/opt/freesurfer/license.txt --fs-no-reconall --use-aroma --ignore fieldmaps
--n_cpus 12 --force-bbr --participant_label $(cat $participants_id) -w
/output
# rm -r /input/$participants_id
done < <(find /input -name "*participants_*" -type f)
echo `rm -r /input/$participants_id`
wait `jobs -p` && echo __ok__ || echo __err__