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-licensesRun 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@hpcLoad 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)