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Uploading from cnt1 to Pennsieve

What this page tells you

To upload from CNT1: ssh to bscsub then CNT1, run 'module load pennsieve', complete the config wizard with your API token/secret, verify with whoami, 'pennsieve dataset use N', create a manifest for the CNT1 folder, and upload it. Page contains an API token/secret.

Credential removed

A password or key that appeared in the original text has been removed. Get it from the lab password manager, never from a wiki page.

Uploading from CNT1 to Pennsieve

  1. Open Terminal
  2. SSH into BSC cluster
  3. SSH into CNT1
    • Once into bsc log into CNT1 with ssh USER@CNT1
  4. Load and Configure Pennsieve Agent or use script command ./pennsieve_setup.sh to do this manually (the setup script's companion page was not migrated)
    • Load module: module load pennsieve
    • Start config wizard: pennsieve config wizard
    • In a separate terminal, get your secret and token with this command: cat .pennsieve/config.ini
    • Enter the api_token and api_secret from your own .pennsieve/config.ini (they are personal; never paste them into a wiki page)
    • Create a new profile bach2 (name it as you wish)
    • Confirm with 'Y'
  5. Verify Pennsieve Login
    • Command: pennsieve whoami
    • Ensure it returns your Pennsieve username
  6. Identify Dataset Number
    • Log in to Pennsieve and find the dataset node ID (N) you want to use
  7. Select the Dataset
    • Command: pennsieve dataset use N
  8. Create a Manifest for Your Folder
    • Command: pennsieve manifest create "cnt1 folder name"
    • Example: pennsieve manifest create "/project/rns/NYU_Neuropace/"
  9. Upload the Manifest
    • Command: pennsieve upload manifest # (replace # with the manifest ID)
  10. (Optional) View Command History
    • Command: history

This version provides a clear, step-by-step guide for transferring files between Pennbox and CNT1, with improved organization and clarity.