FASTA and FASTQ files may be uploaded via the REST API or by using the One Codex CLI or Python client library.
The latter two options are simpler and thus recommended (and also support automatic interleaving and validation of your FASTA/Qs). In every case, we replace spaces in filenames with underscores. To upload with the CLI, simply:
# 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 all FASTQs into your account, # prompting you to interleave any paired end data (recommended) if applicable onecodex upload $LIST_OR_GLOB_OF_YOUR_SAMPLES
Uploading via the REST API consists of 3 steps:
- (1) Initiating an upload by POSTing to
- (2) Uploading the sample to the provided
upload_urland with any
additional_fieldsprovided. See the Starting an Upload documentation for more details.
- (3) Confirming the upload by POSTing to
The above upload mechanisms currently only allow sample uploads up to 20GB (optionally compressed with
gzip). If you need to upload a compressed file over 20GB, please contact us at [email protected] and we can provide an alternative upload or file import mechanism for your situation.