Revert "add new tools"#322
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This reverts commit 1e741d5.
pantherman594
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This change adds back the python libraries removed in #322. Rather than adding them to `CONDA_PACKAGES_2`, we create a third conda environment explicitly for python libraries. This keeps the environments more distinct: one for CLI tools, another for samtools (separated due to dependency version conflicts), and a third for python libraries. The python libraries environment is intended to be the user's main python environment, so we should not need to manipulate `PYTHONPATH`. This python libraries environment can either be an existing environment or a new one. PHP-132843
PeterSu92
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May 21, 2026
PeterSu92
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May 21, 2026
This change adds back the python libraries removed in #322. Rather than adding them to `CONDA_PACKAGES_2`, we create a third conda environment explicitly for python libraries. This keeps the environments more distinct: one for CLI tools, another for samtools (separated due to dependency version conflicts), and a third for python libraries. The python libraries environment is intended to be the user's main python environment, so we should not need to manipulate `PYTHONPATH`. This python libraries environment can either be an existing environment or a new one. PHP-132843
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Reverts #309
This is breaking the Python 3 kernel in our JupyterLab apps with
ImportError: Attempting to import zmq Cython backend, which has not been compiled.because it's searching in the wrong python path