diff --git a/runOpticsTools.sh b/runOpticsTools.sh index 9911050..c74e255 100755 --- a/runOpticsTools.sh +++ b/runOpticsTools.sh @@ -3,27 +3,27 @@ BASEDIR=$(dirname $0) echo "Script location: ${BASEDIR}" -while : -do - echo $1 - case "$1" in - "-offline") offline=$2;; - "-phase") phase=$2;; - esac - shift -done -echo "-offline" -echo $offline -echo "-phase" -echo $phase +if [ -n "$CONDA_PREFIX" ]; then + # Properly deactivate current environment + source $CONDA_PREFIX/etc/conda/deactivate.d/*.sh 2>/dev/null || true +fi -# runs in the sfbd conda environment SLIC -source /sf/bd/packages/conda/etc/profile.d/conda.sh -conda activate slic -export PYTHONPATH=/sf/bd/packages/slic:/sf/bd/packages/sfbd:/sf/bd/packages/bstrd:/sf/bd/packages/pyrealta:/sf/bd/packages/onlinemodel:$PYTHONPATH -cd $BASEDIR -#python OpticsTools.py ${:1} -# needs command line arguments -#-debug 1 -offline 0 +# Reset conda-related environment variables +unset CONDA_PREFIX +unset CONDA_DEFAULT_ENV +unset CONDA_PROMPT_MODIFIER +unset CONDA_SHLVL +# Use the conda executable directly with full path +CONDA_BASE="/sf/bd/packages/miniforge/slic" +# Source conda.sh which properly sets up conda for bash scripts +source $CONDA_BASE/etc/profile.d/conda.sh + +#active conda environmate +conda activate miniforge_sven + +# set path and start python script +export PYTHONPATH=/sf/bd/packages/sfbd:/sf/bd/packages/onlinemodel:$PYTHONPATH +#cd /sf/bd/applications/SynopticViewer/current +python OpticsTools.py -offline 0 -phase 0