Importing data from BaseSpace

You can import data directly from your BaseSpace account using the Upload Page and selecting the option for "Import from: BaseSpace". Once you log in with your BaseSpace credentials, you can select a group of files or projects and import them as a batch.

Programmatic Uploads

To complement the web interface, we also provide a command line interface (CLI) and Python client library for uploading files to One Codex. These tools enable programmatic, including fully automated, uploads to One Codex.

The CLI also supports several additional features:

  • Support for uploads >5GB
  • Automatically combines and interleaves paired-end files into a single sample
  • Saving and reloading API keys / login credentials

Installing the command-line tool

The command line interface is written in Python and accompanies our client library. It should be easily installable on most machines with the following command:

pip install onecodex   # Note, Windows users may need to do `py -m pip install onecodex`

Uploading files

If you haven't previously logged in, the following command will prompt you for your username and password and then save a ~/.onecodex file with your API key.

onecodex login

This command will automatically upload one or more FASTQs into your account, prompting you to interleave any paired-end data if applicable (which we recommend).

onecodex upload Sample1_R1_L001.fastq.gz Sample1_R2_L001.fastq.gz ...

More documentation for the CLI can be found here.

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