diff --git a/docs/developer/getting-started.md b/docs/developer/getting-started.md new file mode 100644 index 0000000000000000000000000000000000000000..942146312e2bac0f1cf2d2bae236033d0bdc3809 --- /dev/null +++ b/docs/developer/getting-started.md @@ -0,0 +1,26 @@ +# Developer - Getting started + +### Requirements +- Maven 3.3 +- Installed Gatk to maven local repository +- Installed Biopet to maven local repository +- + +To start to develop a biopet pipeline you should have installed Gatk and Biopet in your local maven repository. Do to this execute the follow command. +```bash +# Replace 'mvn' for to location of you maven executable or make put it in your PATH +git clone https://github.com/broadgsa/gatk-protected +cd gatk-protected +git checkout 3.4 +# This version is bound to a version of Biopet, Biopet 0.5.0 using Gatk 3.4 +mvn clean install + +cd .. + +git clone https://github.com/biopet/biopet.git +cd biopet +git checkout 0.5.0 +mvn -DskipTests=true clean install + +``` + diff --git a/mkdocs.yml b/mkdocs.yml index fdbcc7b16730d30986641a638a221e8241cb5cf0..14b5690f322dbe199dd7e167b5f5f63ede25ab64 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -38,6 +38,7 @@ pages: - 0.3.1: 'release_notes_0.3.1.md' - 0.3.0: 'release_notes_0.3.0.md' - Developer: + - 'developer/getting-started.md' - 'developer/code-style.md' #- ['developing/Setup.md', 'Developing', 'Setting up your local development environment'] #theme: readthedocs