This project contains a few different tutorials for working with the Galaxy API using blend4j and galaxy-bootstrap, both written by John Chilton. These tutorials assume that you have installed Maven and that you are working with the Eclipse IDE along with the Maven Integration for Eclipse. They also assume some familiarity with Galaxy including a working installation with administrator access. Please see the Get Galaxy guide for more information on how to install Galaxy.
To get started with these tutorials, please run the following command:
$ git clone https://github.com/apetkau/blend4j-tutorials.git
This creates a blend4j-tutorials directory containing the code and other necessary files. This directory is structured like:
$ ls blend4j-tutorials
answers exercises README.md
Each of these subdirectories contains Maven projects with the exercises and answers respectively. To import these projects into eclipse please go to File > Import.... From here select Maven > Existing Maven Projects and click Next. From here click Browse and select the blend4j-tutorials as the root directory. This should list the exercises and answers projects. Please click Finish to import.
The code for each of the exercises should be located within src/main/java or src/test/java. Please follow along below for each of the exercises.
This exercise walks you through adding blend4j to your project and uploading data to a Galaxy library. The tasks are listed withing the pom.xml and src/main/java/Blend4JExercise1.java as 'TODO' comments.
The first step (TODO 1.1) involves adding blend4j to your project within the pom.xml file. Please refer to the Jars section within the blend4j project for more information on what to add.
The remaining TODOs (1.2, 1.3, and 1.4) involve hooking up to your running Galaxy instance and defining the file to upload.
When finished, please go to the Shared Data section of your running Galaxy instance. You should see your newly created Data library along with the uploaded file.
Exercise 1 involved creating a data library using blend4j, then visually looking for this library within the Galaxy web interface. This exercise will re-factor that data library creation code into a test case using JUnit. The code for this exercise, instead of being located within src/main/java, is located within src/test/java/Blend4JExercise2.java.
The first step (TODO 2.1) involes moving some of the setup code to a setup() method that has been annotated with @Before. The second and third steps (TODO 2.2 and 2.3) involve writing Assert statements to programatically verify that the data library was succsessfully created and the file uploaded correctly.
When finished, please run the JUnit test and verify everything passes.
Exercise 2 involved running code against a pre-configured Galaxy and hardcoding a URL and API Key. It would be nice to automate this process by having a clean instance of Galaxy setup each time we wish to run these test suites. This can be accomplished with the galaxy-bootstrap project.
Galaxy bootstrap can be installed by adding the appropriate dependency within the pom.xml file (and Maven will go and download the correct version when necessary). However, I created a fork of galaxy-bootstrap and added a vew extra print statements to help see what's going on behind the scenes. This custom version can be built and installed using the following commands:
$ git clone https://github.com/apetkau/galaxy-bootstrap.git
$ cd galaxy-bootstrap
$ mvn -Dmaven.test.skip=true install
This first clones the customized version of galaxy-bootstrap and then builds the appropriate package (skipping tests since they take a while to run). This package can be found within the target/ directory, for example:
$ ls target/
classes galaxybootstrap-0.3.0-rc2-SNAPSHOT-apetkau.jar generated-sources maven-archiver
Once the package is built it is copied over to your local Maven repository, which on Linux is located within ~/.m2/repository. For example, to see the locally installed package run the following command:
$ ls ~/.m2/repository/com/github/jmchilton/galaxybootstrap/galaxybootstrap/0.3.0-rc2-SNAPSHOT-apetkau
galaxybootstrap-0.3.0-rc2-SNAPSHOT-apetkau.jar galaxybootstrap-0.3.0-rc2-SNAPSHOT-apetkau.pom _maven.repositories
galaxybootstrap-0.3.0-rc2-SNAPSHOT-apetkau.jar.lastUpdated galaxybootstrap-0.3.0-rc2-SNAPSHOT-apetkau.pom.lastUpdated
The path and version number of the package are defined within the galaxybootstrap/pom.xml file and must also be entered as a dependency entry within the blend4j-tutorials/blend4j-tutorial-exercises/pom.xml file. Please copy and paste the following information to blend4j-tutorials/blend4j-tutorial-exercises/pom.xml in order to setup the appropriate dependency (TODO 3.1):
<dependency>
<groupId>com.github.jmchilton.galaxybootstrap</groupId>
<artifactId>galaxybootstrap</artifactId>
<version>0.3.0-rc2-SNAPSHOT-apetkau</version>
</dependency>
More information in building and installing Maven projects can be found at Maven Install Plugin.
Step 2 (TODO 3.2) of this exercise involves creating a new GalaxyInstance by filling in the appropriate URL and API Key within the src/test/java/Blend4JExercise3.java file. This information is obtained from galaxy-bootstrap instead of being hardcoded into a String.
Once you are finished each of the tasks, please run the tests. This will first download the Galaxy code and build Galaxy, then adjust some of the Galaxy settings and start Galaxy running. After this point, the tests will run. Please monitor the Console for information on what is happening.
More examples on how to use blend4j as well as galaxy-bootstrap can be found on the blend4j site as well as the tests for blend4j.