SQLite is a lightweight database management system (DBMS) that can be packaged inside Galaxy and does not require any additional steps at initial setup time. The default out-of-the-box Galaxy installation uses SQLite (). We aren’t going to cover the corresponding object model or object relational mapping. Today we are covering the database and how to access it with SQL. The translation between the two worlds is handled by an object-relational mapping implemented with SQLAlchemy (). The object model is used by the code to manipulate and access the database. The other is the object model which is the object-oriented view of this same data. But that’s only half the picture of the this data. The session description is database centric and we’ll be focusing on the relationalĭatabase that backs Galaxy servers. Quit by: docker kill NAME (you get the name with: docker ps ) Introduction Database versus Object Model Test the Docker image in your web browser: (see first paragraph of Björn’s introduction, for special cases when using theĭocker Toolbox on Mac and Windows). (this will download the Galaxy Docker Image, when executed the first time, and (please do this before the tutorial, preferably when you are still at home using a fast internet connection)įollow the instruction to install the Docker engine: Įxecute: docker run -d -p 8080:80 bgruening/ galaxy-stable Setting up Docker and using the Galaxy Docker Image:
During this tutorial, we will work with the Galaxy Docker Image. You can set-up this yourself, or use the Galaxy Docker Image provided by Björn Grüning ( galaxy-stable). For the hands-on examples you need access to a Galaxy server and access to its PostgreSQL database.
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