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@hpcBefore installing slurmwiz the system_config_file needs creating. There are three variables that need setting; JOB_NAME, IMAGE and TMPDIR, the TMPMYWINEPREFIX should be fine using the pre-filled value.
JOB_NAME: - This should be a character string of the job name that SLURM will use.
IMAGE: - This is a character string of the location of the pwiz sandbox image, you created in the previous step.
TMPDIR: - This is a character string of a directory path that can be used for temporary file creation. It is recommened that this is set to a location in your HPC's scratch space.
One the system_config_file.yml is completem, then the package can be built and installed using the following:
R CMD build slurmwiz
R CMD INSTALL slurmwiz_0.1.1.tar.gz
Load the slurmwiz library and run the slurm_convert function to submit your msconvert job to the SLURM workload manager.
library(slurmwiz)
slurm_convert(input = '/scratch/my_raw_files', output = '/scratch/my_mzml_data', file_ext = 'raw', conversion_args = NULL)