https://github.com/galaxyproject/blend4j

blend4j is a JVM partial reimplementation of the Python library bioblend for interacting with Galaxy, CloudMan, and BioCloudCentral.
https://github.com/galaxyproject/blend4j

Last synced: 3 months ago
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blend4j is a JVM partial reimplementation of the Python library bioblend for interacting with Galaxy, CloudMan, and BioCloudCentral.

• Host: GitHub
• URL: https://github.com/galaxyproject/blend4j
• Owner: galaxyproject
• License: epl-1.0
• Created: 2012-08-20T17:22:45.000Z (about 12 years ago)
• Default Branch: master
• Last Pushed: 2022-10-17T13:24:38.000Z (about 2 years ago)
• Last Synced: 2024-04-09T21:49:23.654Z (7 months ago)
• Language: Java
• Homepage:
• Size: 3.1 MB
• Stars: 16
• Watchers: 22
• Forks: 22
• Open Issues: 12
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE

Awesome Lists containing this project

• awesome-galaxy - Java API bindings

README

        
[![Build Status](https://travis-ci.org/galaxyproject/blend4j.png?branch=master)](https://travis-ci.org/galaxyproject/blend4j)

# About

blend4j is a partial reimplementation of the Python library [bioblend][1]

for the JVM. bioblend for Python is a library for scripting interactions

with Galaxy, CloudMan, and BioCloudCentral.

[1]: https://github.com/afgane/bioblend

# Usage

blend4j's [JavaDocs][api] contain some quick usage examples. Many more

examples can be found in  [Aaron Petkau][apetkau]'s [blend4j tutorials][tutorial]

and the [integration tests][tests]. Examples of using

blend4j in larger open source projects include [Molgenis integration][molgensis] by [Dennis Hendriksen][dennishendriksen] and the

[TraIT Workflow Runner][trait] for use with

[tranSMART][transmart] by [Freek de Bruijn][freekdb].

blend4j requires Java 8+ to function.

[api]: http://galaxyproject.github.io/blend4j/apidocs/

[tutorial]: https://github.com/apetkau/blend4j-tutorials

[tests]: https://github.com/jmchilton/blend4j/tree/master/src/test/java/com/github/jmchilton/blend4j/galaxy

[molgensis]: https://github.com/molgenis/molgenis/commit/57d229a8d36fa9dae1155685e85187399863057f

[transmart]: https://github.com/transmart

[trait]: https://github.com/CTMM-TraIT/trait_workflow_runner

[apetkau]: https://github.com/apetkau

[freekdb]: https://github.com/freekdb

[dennishendriksen]: https://github.com/dennishendriksen

# Building

blend4j can be built with [Apache Maven][b1].

        % git clone git://github.com/galaxyproject/blend4j.git

        % cd blend4j

        % mvn compile

# Testing

[![Build Status](https://travis-ci.org/galaxyproject/blend4j.png?branch=master)](https://travis-ci.org/galaxyproject/blend4j)

blend4j can be tested with [Apache Maven][b1].

        % mvn test 

In this default mode, blend4j will use the [galaxy-bootstrap][t1] 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= -Dtest.galaxy.instance= 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][t2].

[b1]: http://maven.apache.org/

[t1]: https://github.com/jmchilton/galaxy-bootstrap

[t2]: http://maven.apache.org/surefire/maven-surefire-plugin/examples/single-test.html

# 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.

```xml

     

       com.github.jmchilton.blend4j

       blend4j

       0.2.0

     

```

Similar dependencies can be specified if using Ivy, Grape, Gradle, Buildr, or SBT. 

See [mvnrepository][d1] for more details.

The latest blend4j jars can be downloaded from the [Maven Central Repository][d0].

[d0]: http://search.maven.org/#search%7Cga%7C1%7Cg%3A%22com.github.jmchilton.blend4j%22

[d1]: http://mvnrepository.com/artifact/com.github.jmchilton.blend4j/blend4j/

# License

The code is freely available under the [Apache License Version 2.0][l1].

[l1]: http://www.apache.org/licenses/LICENSE-2.0.html