girder-slicer-cli-web 1.0.1.dev21

A girder plugin for exposing slicer CLIs over the web

A Girder plugin for exposing slicer execution model CLIs over the web using docker and girder_worker.

Installation

Slicer CLI Web is both a Girder plugin and a Girder Worker plugin. It allows dockerized tasks to be run from the Girder user interface.

Linux

In linux with Python 2.7, Python 3.5, 3.6, or 3.7:

Prerequisites:

• An appropriate version of Python must be installed.

• MongoDB must be installed and running.

• RabbitMQ or another broker is needed to use Girder Worker.

• Docker must be installed and the current user must be part of the docker group.

To use Girder:

pip install girder-slicer-cli-web[girder]
girder build
girder serve

To use Girder Worker:

pip install girder-slicer-cli-web[worker]
GW_DIRECT_PATHS=true girder_worker -l info -Ofair --prefetch-multiplier=1

The first time you start Girder, you’ll need to configure it with at least one user and one assetstore (see the Girder documentation). Additionally, it is recommended that you install some dockerized taskss, such as the HistomicsTK algorithms. This can be done going to the Admin Console, Plugins, Slicer CLI Web settings. Set a default task upload folder, then import the dsarchive/histomicstk:latest docker image.