Difference between revisions of "SLAW"
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Johnbullard (talk | contribs) (Created page with "Category:Software {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|SLAW}} |{{#vardefine:url|https://github.com/zamboni-lab/SLAW}} <!--CONFIGURATION: OPTIONAL (|1}} means...") |
Johnbullard (talk | contribs) (Add example job script) |
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|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
|{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> | ||
| − | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | + | |{{#vardefine:job|1}} <!--JOB SCRIPTS--> |
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
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<!--Job Scripts--> | <!--Job Scripts--> | ||
{{#if: {{#var: job}}|==Job Script Examples== | {{#if: {{#var: job}}|==Job Script Examples== | ||
| − | + | <pre> | |
| + | #!/bin/bash | ||
| + | #SBATCH --job-name=slaw_test | ||
| + | #SBATCH --mail-type=NONE | ||
| + | #SBATCH --ntasks=1 | ||
| + | #SBATCH --cpus-per-task=8 | ||
| + | #SBATCH --mem=16gb | ||
| + | #SBATCH --time=01:00:00 | ||
| + | #SBATCH --output=slaw_test_%j.log | ||
| + | |||
| + | pwd; hostname; date | ||
| + | |||
| + | module purge | ||
| + | module load slaw | ||
| + | |||
| + | slaw /data/apps/tests/slaw/test_input /data/apps/tests/slaw/test_output | ||
| + | |||
| + | date | ||
| + | </pre> | ||
|}} | |}} | ||
<!--Policy--> | <!--Policy--> | ||
Revision as of 18:14, 4 January 2022
Description
Scalable LC-MS Analysis Workflow
SLAW is a scalable, containerized workflow for untargeted LC-MS processing. It was developed by Alexis Delabriere in the Zamboni Lab at ETH Zurich.
Environment Modules
Run module spider SLAW to find out what environment modules are available for this application.
System Variables
- HPC_SLAW_DIR - installation directory
- HPC_SLAW_BIN - executable directory
Additional Information
UFRC provides a wrapper script for executing the SLAW workflow inside of its container. As such, you should simply call "slaw /path/to/input_dir /path/to/output_dir" from within your job script.
For example:
module load slaw/20211217 slaw /data/apps/tests/slaw/test_input /data/apps/tests/slaw/test_output
This syntax replaces any "docker run ..." or "singularity run ..." commands given in the examples at https://github.com/zamboni-lab/SLAW#quick-start
Job Script Examples
#!/bin/bash #SBATCH --job-name=slaw_test #SBATCH --mail-type=NONE #SBATCH --ntasks=1 #SBATCH --cpus-per-task=8 #SBATCH --mem=16gb #SBATCH --time=01:00:00 #SBATCH --output=slaw_test_%j.log pwd; hostname; date module purge module load slaw slaw /data/apps/tests/slaw/test_input /data/apps/tests/slaw/test_output date
Citation
If you publish research that uses SLAW you have to cite it as follows:
Delabriere A, Warmer P, Brennsteiner V and Zamboni N, SLAW: A scalable and self-optimizing processing workflow for untargeted LC-MS, Anal. Chem. 2021 (https://doi.org/10.1021/acs.analchem.1c02687)