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      • Using Python or Conda environments in the Jupyter App
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      • From Non-compliant Networks (2-FA)
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  • Managing files
    • Oscar's Filesystem
    • Transferring Files to and from Oscar
    • Transferring Files between Oscar and Campus File Storage (Replicated and Non-Replicated)
    • Resolving quota issues
      • Understanding Disk Quotas
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  • Submitting jobs
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    • GPUs on Oscar
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    • Submitting GPU Jobs
    • Intro to CUDA
    • Compiling CUDA
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      • Installing JAX
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  • Large Memory Computing
    • Large Memory Nodes on Oscar
  • Software
    • Software on Oscar
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    • Python on Oscar
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    • Using CCMake
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  • Jupyter Notebooks/Labs
    • Jupyter Notebooks on Oscar
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  • Debugging
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      • Configuring Remote Launch
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  • MATLAB
    • Matlab GUI
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  • Visualization 🕶
    • ParaView Remote Rendering
  • Singularity Containers
    • Intro to Apptainer
    • Building Images
    • Running Images
    • Accessing Oscar Filesystem
      • Example Container (TensorFlow)
    • Singularity Tips and Tricks
  • Installing Software Packages Locally
    • Installing your own version of Quantum Espresso
    • Installing your own version of Qmcpack
  • dbGaP
    • dbGaP Architecture
    • dbGaP Data Transfers
    • dbGaP Job Submission
  • RHEL9 Migration
    • RHEL-9 Migration
    • LMOD - New Module System
    • Module Changes
    • Testing Jupyter Notebooks on RHEL9 mini-cluster
  • Large Language Models
    • Ollama
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  • Downloading new datasets
  • Exporting results data

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  1. dbGaP

dbGaP Data Transfers

The DbGap xfer server is available to import and export data for DbGaP-based projects. Group membership is required for users to log in dbg_import, dbg_export. Connectivity to the xfer server is restricted to Brown networks, remote users will need to first log into the F5 VPN for access. Instructions for downloading new datasets and exporting results are not similar and require different client software.

Downloading new datasets

  • Download and install FastX:

  • Start FastX on your local workstation.

  • Click the “+” icon to create a new entry.

  • Select “SSH”.

  • Enter the connection details:

Host: pdbgxfercit.services.brown.edu

Port: 2223

User: <your Brown username>

  • Click Save.

  • You will be prompted for your password, enter it, and click Continue.

  • You will be prompted to select a Duo authentication method. Enter the number of your choice and click Continue. Confirm your Duo authentication in the manner you selected.

  • After logging in, click the “+” icon to launch a FastX application.

  • Select Desktop and click OK.

  • A Linux Desktop session will launch (this can take several seconds). The Aspera Connect client will be silently installed for your account.

  • Open a web browser or terminal session to download the necessary client software if required.

  • Data sets need to be saved inside the import area to be usable on Oscar.

  • The import area can be accessed from a folder on your desktop, or in ~/import/.

  • In the import area, you can save to your user folder or to any project folder you may have access to.

Exporting results data

  • Download and install Filezilla:

  • Start Filezilla on your local workstation

  • Click File > Site Manager

  • Enter the connection details:

Protocol: SFTP - SSH File Transfer Protocol

Port: 22 (or leave blank)

Host: pdbgxfercit.services.brown.edu

Logon Type: Interactive

User: <your Brown username>

  • Click Connect to begin the login process.

  • Accept the server’s host key by clicking OK.

  • You will be prompted for your password, enter it and click OK.

  • You will be prompted to select a Duo authentication method. Enter the number of your choice and click Continue. Confirm your Duo authentication in the manner you selected.

  • On the Remote site (right) pane, double-click the Results directory.

  • Drag file(s) from the Remote site to your Local filesystem (left) pane.

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Last updated 3 years ago

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https://www.brown.edu/information-technology/software/catalog/fastx
https://www.brown.edu/information-technology/software/catalog/filezilla