A command-line interface for Atmosphere
The Atmosphere CLI is a command-line client written in Python (based on OpenStack’s cliff framework) for Atmosphere. Atmosphere is an integrative, private, self-service cloud computing platform designed to provide easy access to preconfigured, frequently used analysis routines, relevant algorithms, and data sets in an available-on-demand environment designed to accommodate computationally and data-intensive bioinformatics tasks. It is currently in use on the CyVerse and Jetstream projects.
The Atmosphere CLI can be installed from PyPI using pip:
$ pip install atmosphere-cli
There are a few ways to get help. A listing of supported commands and global options can be shown with --help:
$ atmo --help
There is also a help command that can be used to get help for specific commands:
$ atmo help image list
(Optional) Install bash command line completion to get command hints by tabbing:
$ atmo complete >> ~/.bash_aliases $ . ~/.bash_aliases # add to ~/.bashrc or ~/.bash_profile to always load (Ubuntu distro's already load it) $ atmo <tab> allocation group identity instance project size volume complete help image maintenance provider version
The Atmosphere CLI can be configured with environment variables or command-line options. The two required variables are ATMO_BASE_URL, the URL to the corresponding instance of Atmosphere, and ATMO_AUTH_TOKEN, the token needed for authorization. An authorization token can be created by logging into the web client and going to the user menu (upper right corner) and selecting Settings -> Advanced -> Personal Access Tokens. For instance:
export ATMO_BASE_URL="https://atmo.cyverse.org" export ATMO_AUTH_TOKEN="xxxxxxxxxxxxxxxxxxxx"
A sample .env file is provided in the repo. The corresponding command-line options can also be used:
--atmo-base-url <URL> --atmo-auth-token <TOKEN>
To contribute to development and run the included tests:
# grab the repo $ git clone https://github.com/eriksf/atmosphere-cli $ cd atmosphere-cli # install pipenv $ pip install pipenv # install atmosphere-cli $ pipenv install --dev # if multiple python versions installed, select with --python option # setup environment $ cp .env.sample .env # edit ATMO_BASE_URL and ATMO_AUTH_URL as in Configuration section above # load virtual environment $ pipenv shell # this also loads variables in .env to environment
See LICENSE.txt for license information.
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