cryoSPARC v.3.1.0 and Topaz

Particle Picking
5

@jelka @menmt can you try making a bash file that activates your topaz conda environment before invoking topaz? It’ll look something like this:

#!/usr/bin/env bash
# source ~/anaconda/etc/profile.d/conda.sh
conda activate topaz
topaz $@

Optionally remove the # from the beginning of the second line if your conda environment is not automatically activated when the shell starts (then specify the correct path to conda.sh if anaconda is not installed at ~/anaconda)

Save this in your home directory as topaz.sh, then give it execute permissions via command line:

chmod +x ~/topaz.sh

Then in cryoSPARC specify ~/topaz.sh for the “Path to Topaz executable” field and run your job.

If this still leads to the same type of errors, add the following to the top of the topaz.sh, under the #!/usr/bin/env bash line:

if command -v conda > /dev/null 2>&1; then
    conda deactivate > /dev/null 2>&1 || true  # ignore any errors
fi
unset _CE_CONDA
unset CONDA_DEFAULT_ENV
unset CONDA_EXE
unset CONDA_PREFIX
unset CONDA_PROMPT_MODIFIER
unset CONDA_PYTHON_EXE
unset CONDA_SHLVL
unset PYTHONPATH
unset LD_PRELOAD
unset LD_LIBRARY_PATH

This will deactivate cryoSPARC’s Anaconda environment before activating the Topaz environment you installed.

Let me know how that goes.

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