tanu06/sadi-galaxy-docker

Docker image for executing SADI services in a Galaxy server

SADI-Galaxy-Docker

About

SADI is a framework to define Semantic Web Services that consume and output RDF, and SADI-Galaxy makes SADI services available in the popular Galaxy platform. Thus, SADI-Galaxy is a nice SADI client to invoke SADI services in an environment that Biologists use often.

On the other hand, Docker is a sort of "virtualisation" environment for deploying applications very easily, without configuration. Therefore I have created a Docker image for deploying a Galaxy instance already containing SADI-Galaxy, so anyone interested in SADI-Galaxy can try it out easily within having to configure Galaxy and SADI-Galaxy.

Deploying the container

Install Docker and do the thingy for avoiding sudo access:

$ sudo apt-get install docker.io
$ sudo groupadd docker
$ sudo gpasswd -a your_user docker
$ sudo service docker.io restart

(You might need to log out and back in).

Pull the SADI-Galaxy Docker image:

$ docker pull mikeleganaaranguren/sadi-galaxy

Check that it has been succesfully pulled:

$  docker images

REPOSITORY                        TAG                 IMAGE ID            CREATED             VIRTUAL SIZE
mikeleganaaranguren/sadi-galaxy   latest              xxxxxxxxxxx        3 days ago          895.8 MB

Run the container (Make sure that the port 8080 is listening and free in the host machine, or use a different one and map it to the container, e.g. 8389:8080):

$ docker run -d -p 8080:8080 mikeleganaaranguren/sadi-galaxy

If you go with your web browser to http://127.0.0.1:8080 (or the IP of the host machine) there should be a Galaxy server runing. The SADI tools are under SADI services, on the left pane.

Login (in the User menu on the top; user:[email protected], password:useruser) and a history should appear on the right pane.

In the Workflow menu, there is only one workflow, OpenLifeData2SADI SADI. You can have a look by clicking on the workflow name and then clicking edit:

Run the workflow.

Use dataset 1 from the history as input for the workflow (UniProt_IDs.txt).

When the worfklow has finished new steps will appear in the history (20-37).

You can use the workflow, by inspecting the steps, to become familiar with SADI-Galaxy.

Publications mentioning SADI-Galaxy-Docker

Aranguren, M. E. (2015). Merging OpenLifeData with SADI services using Galaxy and Docker (DOI 10.1101/013615). BioRxiv, Cold Spring Harbor Labs doi:10.1101/013615