igboyes / virtool-cli

A command line interface for working with Virtool data

virtool-cli

A command line tool for working with Virtool data.

Installation

pip install virtool-cli

Usage

Build

To build a reference.json file from a src directory

virtool build -src DIRECTORY_PATH -o OUTPUT_PATH

If you wish for the output file to be more easily readable you can specify it to be indented

virtool build -src DIRECTORY_PATH -i

To specify a version to include in the reference.json file

virtool build -src DIRECTORY_PATH -V VERSION

Divide

If you have an existing reference.json you can divide it into a src directory

virtool divide -src REFERENCE_PATH -o OUTPUT_PATH

Taxid

To fetch taxon ids for OTUs in a given src directory that do not currently have one

virtool taxid -src DIRECTORY_PATH

If you wish to force a taxon id lookup for all OTUs

virtool taxid -src DIRECTORY_PATH -f

Environmental Variables

Some of the tools in the CLI make API requests to NCBI. Unauthenticated requests are are limited to 3 per second. Setting NCBI credentials in environmental variables can increase this to 10 per second.

Name	Description
NCBI_EMAIL	The e-mail address used for your NCBI account
NCBI_API_KEY	The API key associated with your NCBI account.