Difference between revisions of "Snakemake"
Jump to navigation
Jump to search
(Created page with "Category:Software {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|Snakemake}} |{{#vardefine:url|https://github.com/snakemake/snakemake}} <!--CONFIGURATION: OPTIONAL (|1...") |
|||
| (5 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
| − | [[Category:Software]] | + | [[Category:Software]][[Category:Workflow Automation]][[Category:Biology]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|Snakemake}} | |{{#vardefine:app|Snakemake}} | ||
| Line 5: | Line 5: | ||
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
| Line 31: | Line 31: | ||
<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | Caveats of running snakemake with SLURM job submission: | |
| − | + | * If you specify a sub-directory for job log file(s) in the snakemake config make sure to create that sub-directory before submitting the main snakemake job as the scheduled jobs will fail immediately if the job log file's directory does not exist. If the path to that directory is 'relative' it is referenced from the path of the working directory, or, if workdir is not specified, from the directory snakemake is executed in. See [https://snakemake.readthedocs.io/en/stable/snakefiles/configuration.html#configure-working-directory Snakemake Working Directory configuration] for more details. | |
|}} | |}} | ||
Latest revision as of 18:51, 15 August 2022
Description
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.
Environment Modules
Run module spider Snakemake to find out what environment modules are available for this application.
System Variables
- HPC_SNAKEMAKE_DIR - installation directory
Additional Information
Caveats of running snakemake with SLURM job submission:
- If you specify a sub-directory for job log file(s) in the snakemake config make sure to create that sub-directory before submitting the main snakemake job as the scheduled jobs will fail immediately if the job log file's directory does not exist. If the path to that directory is 'relative' it is referenced from the path of the working directory, or, if workdir is not specified, from the directory snakemake is executed in. See Snakemake Working Directory configuration for more details.