Commit d36878da authored by Sander Bollen's avatar Sander Bollen Committed by GitHub

Merge pull request #11 from biopet/fix-BIOPET-537

Change develop documentation
parents 36333df3 a695545c
......@@ -5,6 +5,7 @@
Biopet (Bio Pipeline Execution Toolkit) is the main pipeline development framework of the LUMC Sequencing Analysis Support Core team. It contains our main pipelines and some of the command line tools we develop in-house. It is meant to be used in the main [SHARK](https://humgenprojects.lumc.nl/trac/shark) computing cluster. While usage outside of SHARK is technically possible, some adjustments may need to be made in order to do so.
Full documantation is here: [Biopet documantation](http://biopet-docs.readthedocs.io/en/latest/)
## Quick Start
......@@ -48,9 +49,9 @@ $ biopet pipeline <pipeline_name> -config <path/to/config.json> -qsub -jobParaEn
It is usually a good idea to do the real run using `screen` or `nohup` to prevent the job from terminating when you log out of SHARK. In practice, using `biopet` as it is is also fine. What you need to keep in mind, is that each pipeline has their own expected config layout. You can check out more about the general structure of our config files [here](docs/config.md). For the specific structure that each pipeline accepts, please consult the respective pipeline page.
### Running Biopet in your own computer
## Testing
At the moment, we do not provide links to download the Biopet package. If you are interested in trying out Biopet locally, please contact us as [sasc@lumc.nl](mailto:sasc@lumc.nl).
Our code is tested at our local Jenkins installation for every change. We are using a [JenkinsFile](Jenkinsfile) in our repository to do this.
## Contributing to Biopet
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We welcome any kind of contribution, be it merge requests on the code base, documentation updates, or any kinds of other fixes! The main language we use is Scala, though the repository also contains a small bit of Python and R. Our main code repository is located at [https://github.com/biopet/biopet](https://github.com/biopet/biopet/issues), along with our issue tracker.
## Local development setup
To develop Biopet, Java 7, Maven 3.3.3, and GATK Queue 3.5 is required. Please consult the Java homepage and Maven homepage for the respective installation instruction. After you have both Java and Maven installed, you would then need to install GATK Queue. However, as the GATK Queue package is not yet available as an artifact in Maven Central, you will need to download, compile, and install GATK Queue first.
~~~
$ git clone https://github.com/broadgsa/gatk-protected
$ cd gatk
$ git checkout 3.5 # the current release is based on GATK 3.5
$ mvn -U clean install
~~~
This will install all the required dependencies to your local maven repository. After this is done, you can clone our repository and test if everything builds fine:
~~~
$ git clone https://github.com/biopet/biopet.git
$ cd biopet
$ mvn -U clean install
~~~
If everything builds fine, you're good to go! Otherwise, don't hesitate to contact us or file an issue at our issue tracker.
For more information please go to our [Developer documantation](http://biopet-docs.readthedocs.io/en/develop/developer/getting-started/)
## About
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### Requirements
- Maven 3.3
- Java 8
- Installed Gatk to maven local repository (see below)
- Installed Biopet to maven local repository (see below)
- Some knowledge of the programming language [Scala](http://www.scala-lang.org/) (The pipelines are scripted using Scala)
......@@ -16,17 +17,9 @@ Make sure both tools are installed in your local maven repository. To do this on
```bash
# Replace 'mvn' with the location of you maven executable or put it in your PATH with the export command.
git clone https://github.com/broadgsa/gatk
cd gatk
git checkout 3.6
# The GATK version is bound to a version of Biopet. Biopet 0.7.0 uses Gatk 3.6
mvn clean install
cd ..
git clone https://github.com/biopet/biopet.git
git clone --recursive https://github.com/biopet/biopet.git
cd biopet
git checkout 0.7.0
mvn -DskipTests=true clean install
```
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