SLAW and Singularity


What is SLAW?

SLAW is a scalable, containerized workflow untargeted LC-MS processing. It was developed by Alexis Delabriere in the Zamboni Lab at ETH Zurich. An explanation of the advantages of SLAW and its motivations of development can be found in this blog post. In brief, the core advantages of SLAW are:

Getting the Test Data from the Source Code

You may want to download the SLAW Source Code which contains some test data you can test for your SLAW Container.

% git clone https://github.com/zamboni-lab/SLAW.git

Let make a new directory my_SLAW and copy the test_data out. I’m assuming you have Singularity Installed. Compiling Singularity-CE-3.9.2 on CentOS-7.

Create the output folder and unzip the MzmL.zip

% cp SLAW/test_data ~my_SLAW
% cd ~my_SLAW/test_data
% mkdir output
% unzip mzML.zip
% singularity pull slaw.sif docker://zambonilab/slaw:latest

Test Runing. Just a few things to note. Try to use the absolute PATH for PATH_OUTPUT and MZML_Folder

% singularity run -C -W . -B PATH_OUTPUT:/output  -B MZML_FOLDER:/input slaw.sif

For example,

% singularity run -C -W . -B /home/user1/my_SLAW/output:/output  -B /home/user1/my_SLAW/mzmL:/input slaw.sif
2022-02-25|00:46:52|INFO: Total memory available: 53026 and 32 cores. The workfl
2022-02-25|00:46:52|INFO: Guessing polarity from file:DDA1.mzML
2022-02-25|00:46:53|INFO: Polarity detected: positive
2022-02-25|00:46:54|INFO: STEP: initialisation TOTAL_TIME:2.41s LAST_STEP:2.41s
2022-02-25|00:46:55|INFO: 0 peakpicking added
2022-02-25|00:46:59|INFO: MS2 extraction finished
2022-02-25|00:46:59|INFO: Starting peaktable filtration
2022-02-25|00:46:59|INFO: Done peaktables filtration
2022-02-25|00:46:59|INFO: STEP: peakpicking TOTAL_TIME:7.57s LAST_STEP:5.16s
2022-02-25|00:46:59|INFO: Alignment finished
2022-02-25|00:46:59|INFO: STEP: alignment TOTAL_TIME:7.60s LAST_STEP:0.03s
2022-02-25|00:47:10|INFO: Gap filling and isotopic pattern extraction finished.
2022-02-25|00:47:10|INFO: STEP: gap-filling TOTAL_TIME:18.01s LAST_STEP:10.41s
2022-02-25|00:47:10|INFO: Annotation finished
2022-02-25|00:47:10|INFO: STEP: annotation TOTAL_TIME:18.04s LAST_STEP:0.03s
2022-02-25|00:47:10|INFO: Processing finished.

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