ASaiM framework

ASaiM framework is an open-source opinionated Galaxy-based framework. It integrates tools, specifically chosen for metagenomic and metatranscriptomic studies and hierarchically organized to orient user choice toward the best tool for a given task.

Details about this framework is available on a dedicated documentation available at http://asaim.readthedocs.org/.

This framework is using the Galaxy Docker to ease the deployment the Galaxy instance.

Usage

Requirements

To use the ASaiM framework, Docker is required

For Linux users and people familiar with the command line, please follow the very good instructions from the Docker project. Non-Linux users are encouraged to use Kitematic, a graphical User-Interface for managing Docker containers.

The databases used by HUMAnN2 are quite big, we recommend to have at least 100 Gb of disk space

ASaiM launch

1. Starting the ASaiM Docker container: analogous to starting the generic Galaxy Docker image:

   $ docker run -d -p 8080:80 quay.io/bebatut/asaim-framework
   

   Nevertheless, here is a quick rundown:

   • docker run starts the Image/Container

     In case the Container is not already stored locally, Docker downloads it automatically

   • The argument -p 8080:80 makes the port 80 (inside of the container) available on port 8080 on your host

     Inside the container a Apache web server is running on port 80 and that port can be bound to a local port on your host computer. With this parameter you can access your Galaxy instance via http://localhost:8080 immediately after executing the command above

   • quay.io/bebatut/asaim-framework is the Image/Container name, that directs Docker to the correct path in the Docker index

   • -d will start the Docker container in Daemon mode.

   A detailed discussion of Docker's parameters is given in the Docker manual. It is really worth reading.

   The Docker container is run: Galaxy will be launched!

   Setting up Galaxy and its components can take several minutes. You can inspect the state of the starting using:

   $ docker ps # to obtain the id of the container
   $ docker logs <container_id>
   

   The previous commands will start the ASaiM framework with the configuration and launch of a Galaxy instance and its population with the needed tools, workflows and databases. The instance will be accessible at http://localhost:8080.

2. Installation of the databases once Galaxy is running

   $ docker exec <container_id> ./run_data_managers
   

Usage: workflows, databases, data, etc.

More details about the installation of ASaiM and its usage can be found on the online documentation

Documentation

Available tools and workflows in ASaiM framework are described in the documentation available at http://asaim.readthedocs.org/. It comes also with tutorials.

Bug Reports

Any bug can be filed in an issue here.

License

ASaiM framework is released under Apache 2 License. See the LICENSE file for details.

Contributing

How to Contribute:

• Make sure you have a GitHub account
• Make sure you have git installed
• Fork the repository on GitHub
• Make the desired modifications - consider using a feature branch
• Open a pull request with these changes.

Thanks!

Citation

If you use this tool, please cite:

ASaiM: a Galaxy-based framework to analyze raw shotgun data from microbiota
Bérénice Batut, Kévin Gravouil, Clémence Defois, Saskia Hiltemann, Jean-François Brugère, Eric Peyretaillade, Pierre Peyret
bioRxiv 183970; doi: https://doi.org/10.1101/183970