Skip to content

Commit

Permalink
Browse files Browse the repository at this point in the history
docs: Clarify the use of conda with notebook directive (#1515)
* Clarify the use of conda with notebook directive

* Update deployment.rst
  • Loading branch information
SultanOrazbayev committed Mar 24, 2022
1 parent 1364dfb commit aefb1eb
Showing 1 changed file with 2 additions and 2 deletions.
4 changes: 2 additions & 2 deletions docs/snakefiles/deployment.rst
Expand Up @@ -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.
Expand Down

0 comments on commit aefb1eb

Please sign in to comment.