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@@ -15,7 +16,7 @@ Sunbeam currently automates the following tasks:
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* Taxonomic assignment of reads to databases using [Kraken](https://github.com/DerrickWood/kraken) ([sbx_kraken](https://github.com/sunbeam-labs/sbx_kraken));
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* Assembly of reads into contigs using [Megahit](https://github.com/voutcn/megahit) ([sbx_assembly](https://github.com/sunbeam-labs/sbx_assembly));
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* Contig annotation using BLAST[n/p/x] and Diamond ([sbx_assembly](https://github.com/sunbeam-labs/sbx_assembly));
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* Mapping to reference genomes ([sbx_mapping](https://))
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* Mapping to reference genomes ([sbx_mapping](https://github.com/sunbeam-labs/sbx_mapping))
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* ORF prediction using [Prodigal](https://github.com/hyattpd/Prodigal) ([sbx_assembly](https://github.com/sunbeam-labs/sbx_assembly)).
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More extensions can be found at https://github.com/sunbeam-labs.
Copy file name to clipboardexpand all lines: docs/examples.rst
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#SBATCH --no-requeue
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#SBATCH --output=slurm_%x_%j.out
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# Conda env must be activate for this to work
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# Conda env must be active for this to work
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set -x
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set -e
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sunbeam run --profile /projects/my_project all_assembly
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Including any other database in a containerized run is as simple as mounting the database directory into the container and pointing to it in the config file. For example, if you have a kraken database in ``/kraken_db`` and you want to use it in a containerized run, you would add ``-v /kraken_db:/kraken_db`` to the ``docker run`` command and then set the ``kraken_db_fp`` parameter in the config file to ``/kraken_db`` (after installing ``sbx_kraken``).
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Using Slurm with the Containerized Install and Containerized Environments
This is a combination of all of the above. You have a dataset on your institution's HPC (which uses slurm to manage jobs) and you want to run sunbeam to automate qc, decontam, and assembly of metagenomic contigs. Your data is paired end and lives in a directory called ``/data``. You have singularity available on the cluster and you want to use containerized environments (apptainer or similar solutions also work). Run:
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.. code-block:: bash
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### FIND AND LOAD SINGULARITY MODULE IF IT ISN'T ALREADY LOADED ###
vi /projects/my_project/config.yaml # edit the config file to make any desired changes (including switching ``software-deployment-method`` to ``apptainer``)
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.. note::
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Setting the ``SINGULARITY_TMPDIR`` environment variable may be necessary to avoid a bug in singularity that causes it to fail when running snakemake. The path should be a directory that is writable by the user running the container and large enough not to run out of space.
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Now you're ready to run the project, but you want to be able to put the main node on the cluster as well so you can logoff, so you create a bash script called ``run_sunbeam.sh``:
Copy file name to clipboardexpand all lines: docs/structure.rst
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-----
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This directory contains ``.yml`` files defining environments that will be managed by snakemake as it runs. Anywhere that a rule is defined with ``conda: /path/to/ENV_NAME.yml``, when snakemake reaches that rule, that environment will be created if it doesn't exist already and then activated while running the rule. These environments are created in ``sunbeam/.snakemake/`` by default.
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The accompanying files named something like ``ENV_NAME.ARCH.pin.txt`` are generated with ``snakedeploy``. They list all the packages and exact versions in a given environment (for the architecture they were generated on, e.g. linux-64) so that snakemake can first try to use that exact environment and only if it fails, try to solve the ``.yml`` file for itself.
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There may be accompanying files named something like ``ENV_NAME.ARCH.pin.txt`` which are generated with ``snakedeploy``. They list all the packages and exact versions in a given environment (for the architecture they were generated on, e.g. linux-64) so that snakemake can first try to use that exact environment and only if it fails, try to solve the ``.yml`` file for itself.
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