Environment Variables

nimble uses several environment variables:

TMPDIR

Configures the directory to put temporary files for samtools sorting. By default, they're placed in the current working directory. It's recommended that you do not set this to /tmp -- depending on the size of the input dataset, the volume of temporary files is too large for a standard /tmp configuration.

NCBI_EMAIL

Sets the email to be attached to NCBI Genbank API requests. Highly recommended that you set this, so that the NCBI can contact you if there are issues with your API usage.

NCBI_API_KEY

A valid NCBI API key. Highly recommended that you set this if the standard anonymous data rate is too slow for your use-case.