diff --git a/toil_examples/source_selection.sh b/toil_examples/source_selection.sh index 39502c5b..530681e7 100644 --- a/toil_examples/source_selection.sh +++ b/toil_examples/source_selection.sh @@ -1,6 +1,6 @@ #!/bin/bash -#NOTE: WORKS ONLY FROM TOIL>6.0.0 +#NOTE: works only with TOIL>6.0.0 #### UPDATE THESE #### @@ -27,13 +27,13 @@ if [[ "$CONTAINERSTR" == *"apptainer"* ]]; then export APPTAINER_TMPDIR=$APPTAINER_CACHEDIR/tmp export APPTAINER_PULLDIR=$APPTAINER_CACHEDIR/pull export APPTAINER_BIND=$SING_BIND - export APPTAINERENV_PYTHONPATH='$VLBI_SCRIPTS:$PYTHONPATH' + export APPTAINERENV_PYTHONPATH='${VLBI_SCRIPTS}:$PYTHONPATH' else export SINGULARITY_CACHEDIR=$PWD/singularity export SINGULARITY_TMPDIR=$SINGULARITY_CACHEDIR/tmp export SINGULARITY_PULLDIR=$SINGULARITY_CACHEDIR/pull export SINGULARITY_BIND=$SING_BIND - export SINGULARITYENV_PYTHONPATH='$VLBI_SCRIPTS:$PYTHONPATH' + export SINGULARITYENV_PYTHONPATH='${VLBI_SCRIPTS}:$PYTHONPATH' fi export CWL_SINGULARITY_CACHE=$APPTAINER_CACHEDIR