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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: about 2 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 (almost 2 years ago)
- Last Synced: 2024-04-09T21:49:23.654Z (5 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
[](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
[](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