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BCCDC-DSI / RADD

Consult at the BCCDC for Mass Spectrometry
MIT License
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Replicating `nps-screening` #1

Closed Afraz496 closed 2 months ago

Afraz496 commented 2 months ago

After following the steps to make the apptainer (successful) encountering the following error:

Warning message:
In dir.create(output_dir) :
  cannot create dir '/xcms', reason 'Read-only file system'
[1] "sh_file /arc/project/st-cfjell-1/git/nps-screening//sh/write-ms1-matches-xcms.sh"
[1] "grid_file, sh/grids/write-ms1-matches-xcms.txt"
Error in read.table(file = file, header = header, sep = sep, quote = quote,  :
  no lines available in input
Calls: write_sh -> read.delim -> read.table
Execution halted
Apptainer> export NPS_GIT_ROOT=/arc/project/st-cfjell-1/git/nps-screening/

Either the apptainer in the folder isn't properly specified or this user (mine) only has Read privileges on files and not write privileges.

Afraz496 commented 2 months ago

Decided that this approach was not necessary for replication (DEFUNCT)