thehyve/blend4j

Name: blend4j

Owner: The Hyve

Description: blend4j is a JVM partial reimplemenation of the Python library bioblend for interacting with Galaxy, CloudMan, and BioCloudCentral.

Created: 2014-03-18 10:46:15.0

Updated: 2014-07-21 09:20:44.0

Pushed: 2014-07-21 09:20:43.0

Homepage:

Size: 385

Language: Java

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README

About

blend4j is a partial reimplemenation of the Python library bioblend for the JVM. bioblend for Python is a library for scripting interactions with Galaxy, CloudMan, and BioCloudCentral.

Usage

blend4j's JavaDocs contain some quick usage examples. Many more examples can be found in Aaron Petkau's blend4j tutorials and the integration tests. Examples of using blend4j in larger open source projects include Molgenis integration by Dennis Hendriksen and the TraIT Workflow Runner for use with tranSMART by Freek de Bruijn.

Building

blend4j can be built with Apache Maven.

    % git clone git://github.com/jmchilton/blend4j.git
    % cd blend4j
    % mvn compile

Testing

blend4j can be tested with Apache Maven.

    % mvn test 

In this default mode, blend4j will use the galaxy-bootstrap library to download, configure, and run an instance of Galaxy for testing (requiring an Internet connection). blend4j can be tested against an existing instance using the following Java system properties.

    % mvn -Dtest.galaxy.key=<key> -Dtest.galaxy.instance=<url> test

The above example will run a variety of tests and make various assumptions - some which may not be true for the supplied API key. Maven can be configured to run a specific test or tests.

Jars

The easiest way to obtain blend4j is using Maven Central.

For instance, if a project is using Maven, a blend4j dependency can be added by adding the following to the dependencies section of the project's pom.xml file.

 <dependency>
   <groupId>com.github.jmchilton.blend4j</groupId>
   <artifactId>blend4j</artifactId>
   <version>0.1.0</version>
 </dependency>

Similar dependencies can be specified if using Ivy, Grape, Gradle, Buildr, or SBT. See mvnrepository for more details.

The latest blend4j jars can be downloaded from the Maven Central Repository.

License

The code is freely available under the Apache License Version 2.0.