virtool-cli

A command line tool for working with Virtool data.

Installation

git clone https://github.com/virtool/virtool-cli.git
pip install .

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 requests to NCBI databases, which are usually rate-limited to 3 requests/second. If you are working with larger directories this will cause some tools to run extremely slowly. Fortunately, with correct authenication this limit can be raised to 10 requests/second. This involves setting up the following environmental variables:

NCBI_EMAIL - The e-mail address used for your NCBI account

NCBI_API_KEY - The API key associated with your NCBI account. If you are currently signed into NCBI it can be found here.