diff --git a/docs/developer/getting-started.md b/docs/developer/getting-started.md index 942146312e2bac0f1cf2d2bae236033d0bdc3809..744237ac0f9e77ba9c1d6477cd49a0a60775d169 100644 --- a/docs/developer/getting-started.md +++ b/docs/developer/getting-started.md @@ -2,9 +2,8 @@ ### Requirements - Maven 3.3 -- Installed Gatk to maven local repository -- Installed Biopet to maven local repository -- +- Installed Gatk to maven local repository (see below) +- Installed Biopet to maven local repository (see below) 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 @@ -24,3 +23,12 @@ mvn -DskipTests=true clean install ``` +### Basic components + +#### Qscript (pipeline) +A basic pipeline would look like this. + +#### Extensions (wrappers) + + +#### Tools (scala programs) \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index 14b5690f322dbe199dd7e167b5f5f63ede25ab64..f065caa1f1a9fe7bfb3d231fee6df23eb5a0626c 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -38,8 +38,10 @@ 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' + - Getting Started: 'developer/getting-started.md' + - Code Style: 'developer/code-style.md' + - Scala docs: + - 0.4.0: 'developer/code-style.md' #- ['developing/Setup.md', 'Developing', 'Setting up your local development environment'] #theme: readthedocs repo_url: https://github.com/biopet/biopet