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docs: Clarify the use of conda with notebook directive (#1515)
* Clarify the use of conda with notebook directive

* Update deployment.rst
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SultanOrazbayev committed Mar 24, 2022
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@@ -275,8 +275,8 @@ Instead of using a concrete path, it is also possible to provide a path containi

.. sidebar:: Note

Note that conda environments are only used with ``shell``, ``script`` and the ``wrapper`` directive, not the ``run`` directive.
The reason is that the ``run`` directive has access to the rest of the Snakefile (e.g. globally defined variables) and therefore must be executed in the same process as Snakemake itself.
Note that conda environments are only used with ``shell``, ``script``, ``notebook`` and the ``wrapper`` directive, not the ``run`` directive.
The reason is that the ``run`` directive has access to the rest of the Snakefile (e.g. globally defined variables) and therefore must be executed in the same process as Snakemake itself. If used with ``notebook`` directive, the associated conda environment should have package ``jupyter`` installed (this package contains dependencies required to execute the notebook).

Further, note that search path modifying environment variables like ``R_LIBS`` and ``PYTHONPATH`` can interfere with your conda environments.
Therefore, Snakemake automatically deactivates them for a job when a conda environment definition is used.

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