Difference between revisions of "SLAW"

Latest revision as of 23:49, 21 August 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)

@@ Line 1: / Line 1: @@
-[[Category:Software]]
+[[Category:Software]][[Category:Chemistry]][[Category:Spectroscopy]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|SLAW}}
@@ Line 6: / Line 6: @@
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
 |{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
-|{{#vardefine:job|}}            <!--JOB SCRIPTS-->
+|{{#vardefine:job|1}}            <!--JOB SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
 |{{#vardefine:testing|}}       <!--PROFILING-->
@@ Line 46: / Line 46: @@
 <!--Job Scripts-->
 {{#if: {{#var: job}}|==Job Script Examples==
-See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} 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-->