yuch7 / cwlexec

A new open source tool to run CWL workflows on LSF
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dockerOptions.sh as documented fails on short options #71

Open fthommen opened 1 year ago

fthommen commented 1 year ago

the pre-exec script dockerOptions.sh

#!/bin/bash
for OPTION in $LSB_CONTAINER_OPTIONS
do
    echo $OPTION
done

works fine with long options (--env=VAR=value) but fails with short options (-e VAR=value) due to the whitespace between option and value. Instead it should simply print out $LSB_CONTAINER_OPTIONS as-is:

#!/bin/bash
echo "$LSB_CONTAINER_OPTIONS"