Command lines and libraries

The ATLAS-D2K repository can be accessed programmatically through command line interfaces and libraries.

Libraries

• python client library
• R client library
• js client library

Deriva Client tools

Install deriva-client:

• For folks that have python3 installed run: pip install deriva-client
• For Windows/Mac users who want bundles, download here: https://github.com/informatics-isi-edu/deriva-client-bundle/releases/latest
• General information on deriva-client here: https://github.com/informatics-isi-edu/deriva-client

Command lines

Download an exported BDBAG through command lines

• Download and install Deriva.py
• Download the appropriate export configs
  • RNASeq Replicates
  • Note: all our configs can be found here.
• Run the deriva-download-cli commands:

  usage: deriva-download-cli [-h] [--version] [--quiet] [--debug]
                           [--credential-file <file>]
                           [--token <auth-token> | --oauth2-token <oauth2-token>]
                           [--catalog <1>]
                           <host> <config file> <output dir> [<key=value key=value>]
  

  For example:

  > mkdir deriva-downloads
  > deriva-download-cli www.atlas-d2k.org --catalog 2 ./replicate_export_config.json ./deriva-downloads rid=16-1ZX4