wilsontom/slurmwiz

Convert Mass Spectrometry Files using msconvert, singularity and SLURM

slurmwiz

Getting Started

Before installing the slurmwiz R package, the pwiz singularity sandbox needs creating. To do this, you need to be using a linux filesystem which has docker and singularity installed.

singularity build --sandbox pwiz_sandbox docker://chambm/pwiz-skyline-i-agree-to-the-vendor-licenses

Run the following command to make sure that the sandbox is working coorrectly

singularity exec -w pwiz_sandbox wine msconvert 

The sandbox than then be archived, transfered onto your HPC.

tar --create --file pwiz_sandbox.tar pwiz_sandbox 
scp pwiz_sandbox.tar user@hpc

Converting Files

Load the slurmwiz library and run the slurm_convert function to submit your msconvert job to the SLURM workload manager.

library(slurmwiz)

slurm_convert(data_in = '/scratch/my_raw_files', save_path = '/scratch/my_mzml_data', file_ext = 'raw', conversion_args = NULL)