Installation¶
Snakeface can be installed and run from a virtual environment, or from a container.
Virtual Environment¶
First, clone the repository code.
$ git clone git@github.com:snakemake/snakeface.git
$ cd snakeface
Then you’ll want to create a new virtual environment, and install dependencies.
$ python -m venv env
$ source env/bin/activate
$ pip install -r requirements.txt
And install Snakeface (from the repository directly)
$ pip install -e .
Install via pip¶
Snakeface can also be installed with pip.
$ pip install snakeface
Once it’s installed, you should be able to inspect the client!
$ snakeface --help
usage: snakeface [-h] [--version] [--noreload] [--verbosity {0,1,2,3}]
[--workdir [WORKDIR]] [--auth {token}] [--port PORT]
[--verbose] [--log-disable-color] [--log-use-threads]
[--force]
[repo] [dest] {notebook} ...
Snakeface: interface to snakemake.
positional arguments:
repo Repository address and destination to deploy, e.g.,
<source> <dest>
dest Path to clone the repository, should not exist.
optional arguments:
-h, --help show this help message and exit
--version print the version and exit.
--noreload Tells Django to NOT use the auto-reloader.
--verbosity {0,1,2,3}
Verbosity (0, 1, 2, 3).
--workdir [WORKDIR] Specify the working directory.
--force If the folder exists, force overwrite, meaning remove
and replace.
SETTINGS:
--auth {token} Authentication type to create for the interface,
defaults to token.
NETWORKING:
--port PORT Port to serve application on.
LOGGING:
--verbose verbose output for logging.
--log-disable-color Disable color for snakeface logging.
--log-use-threads Force threads rather than processes.
actions:
subparsers for Snakeface
{notebook} snakeface actions
notebook run a snakeface notebook
Setup¶
As a user, you most likely want to use Snakeface as an on demand notebook, so no additional setup is needed other than installing the package. As we add more deployment types that warrant additional configuration, or in the case of installing Snakeface as a cluster admin, you likely will want to install from the source repository (or a release) and edit the settings.yml file in the snakemake folder before deploying your service. More information will be added as this is developed. If you are interested, you can look at Settings.