From aefb1eb0a2d62faa6108670f3a11d58a1d797c41 Mon Sep 17 00:00:00 2001 From: Sultan Orazbayev Date: Fri, 25 Mar 2022 00:12:56 +0600 Subject: [PATCH] docs: Clarify the use of conda with notebook directive (#1515) * Clarify the use of conda with notebook directive * Update deployment.rst --- docs/snakefiles/deployment.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/snakefiles/deployment.rst b/docs/snakefiles/deployment.rst index 5f12e6a4e..6835d6e30 100644 --- a/docs/snakefiles/deployment.rst +++ b/docs/snakefiles/deployment.rst @@ -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.