From 883abceb9a1af140cb2ae262d3e78f2b8b5d4aa6 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 23 Sep 2015 20:45:18 +0200
Subject: [PATCH] Adding getting started
---
docs/developer/getting-started.md | 26 ++++++++++++++++++++++++++
mkdocs.yml | 1 +
2 files changed, 27 insertions(+)
create mode 100644 docs/developer/getting-started.md
diff --git a/docs/developer/getting-started.md b/docs/developer/getting-started.md
new file mode 100644
index 000000000..942146312
--- /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 fdbcc7b16..14b5690f3 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
--
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