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Download CosMx Data directly to BMRC from AtoMx ServerΒΆ

Note

  • You will need an AtoMx Platform account to download this data. Discuss the account details with KIR Spatial/SingleCell SRF Manager/s
  • Highly recommend using a tmux session for this download as it can from few minutes to hours
  • Replace /Remote_Directory_Name with the directory name on AtoMx export panel. Make sure to include leading slash /
  • Replace /path/in/bmrc/filesystem/ with the path BMRC. Make sure to include trailing slash
  • When you execute the following command block with the adjusted paths, it will prompt for AtoMx Password:
module load lftp

lftp -u username@kennedy.ox.ac.uk sftp://eu.export.atomx.nanostring.eu -e "
set sftp:connect-program 'ssh -o PubkeyAuthentication=no -o PreferredAuthentications=password -a -x';
set net:timeout 30;
set net:max-retries 5;
set net:reconnect-interval-base 5;
mirror -c --verbose --use-pget-n=3 /Remote_Directory_Name /path/in/bmrc/filesystem/;
bye"