diff --git a/docs/source/WORKFLOWS.rst b/docs/source/WORKFLOWS.rst index d31ba6a..653af9b 100644 --- a/docs/source/WORKFLOWS.rst +++ b/docs/source/WORKFLOWS.rst @@ -139,6 +139,7 @@ For local or HPC mode, CulebrONT can be run using a typical ``snakemake`` comman .. code-block:: bash + -v : enable verbose mode (default disable) -c option : config.yaml file -k option : cluster_config.yaml -p option : profile path @@ -152,11 +153,11 @@ If you are on LOCAL mode, give at least the -c option to ``submit_culebront.sh`` .. code-block:: bash # in LOCAL using maximum 8 threads - submit_culebront.sh -c config.yaml -a "--cores 8 " + submit_culebront.sh -v -c config.yaml -a "--cores 8 " # in LOCAL using 6 threads for Canu assembly from the total 8 threads - submit_culebront.sh -c config.yaml -a "--cores 8 --set-threads run_canu=6" - submit_culebront.sh -c config.yaml -a '--cores 8' + submit_culebront.sh -v -c config.yaml -a "--cores 8 --set-threads run_canu=6" + submit_culebront.sh -v -c config.yaml -a '--cores 8' .. note:: @@ -167,21 +168,31 @@ Running in a HPC If you are on HPC mode, give to ``submit_culebront.sh`` at least the -c option and -p options to the ``submit_culebront.sh`` script. You can use profiles to manage cluster resources. Go to :ref:`3. Snakemake profiles` for details OR ask to your admin system where CulebrONT profile was created. + +If you install on HPC with module envs :ref:`4. Export CulebrONT to PATH`, you can directly use + .. code-block:: bash - # declare profile path directory - profile=/directory/of/culebront/profile/ # in HPC using cluster_config.yaml directly from profile - submit_culebront.sh -c config.yaml --profiles $profile + submit_culebront.sh -c config.yaml --profiles $PROFILE + +where `$PROFILE` is declare on module file. If you doesn't use module envs please declare `$PROFILE` + +.. code-block:: bash + + # declare profile path directory + PROFILE=/directory/of/culebront/profile/ + submit_culebront.sh -c config.yaml --profiles $PROFILE + If cluster default resources are not sufficient, you can overwrite ``cluster_config.yaml`` file used by the profile. You can use -k option to overwrite cluster resources. .. code-block:: bash # in HPC mode, overwriting cluster_config.yaml given by user - submit_culebront.sh -c config.yaml -k cluster_config.yaml --profiles $profile + submit_culebront.sh -c config.yaml -k cluster_config.yaml --profiles $PROFILE # in HPC mode, overwriting cluster_config.yaml given by user and launch a --dryrun - submit_culebront.sh -c config.yaml -k cluster_config.yaml --profiles $profile -a '--dryrun' + submit_culebront.sh -c config.yaml -k cluster_config.yaml --profiles $PROFILE -a '--dryrun' .. note:: Using ``submit_culebront.sh`` you can optionally pass to snakemake more options by using the -a parameter (check it https://snakemake.readthedocs.io/en/stable/executing/cli.html).