From c4834a47d06632cde62021a5465dcc3a8fedac2c Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <sajvanderzeeuw@sasc-sander.lumcnet.prod.intern>
Date: Fri, 14 Nov 2014 16:08:23 +0100
Subject: [PATCH] added docs

---
 docs/about.md   | 11 +++++++++-
 docs/index.md   | 53 +++++++++++++++++++++++++++++++++++++++++++++++--
 docs/license.md |  3 +--
 3 files changed, 62 insertions(+), 5 deletions(-)

diff --git a/docs/about.md b/docs/about.md
index 6ca1a0ded..884f30e87 100644
--- a/docs/about.md
+++ b/docs/about.md
@@ -10,8 +10,17 @@ platform and reduce code duplication and increase maintainability.
 
 
 ## The Team
+SASC:
+Currently our team excists out of 5 members
 
+- Leon Mei (LUMC-SASC) 
+- Wibowo Arindrarto (LUMC-SASC)
+- Peter van 't Hof (LUMC-SASC)
+- Wai Yi Leung (LUMC-SASC)
+- Sander van der Zeeuw (LUMC-SASC)
 
 ## Contact
 
-We even have a website: https://sasc.lumc.nl/
\ No newline at end of file
+check our website at: [SASC](https://sasc.lumc.nl/)
+
+We are also reachable through email: [SASC mail](mailto:SASC@lumc.nl)
\ No newline at end of file
diff --git a/docs/index.md b/docs/index.md
index 65d91319d..e55d0941f 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -1,5 +1,54 @@
 # Welcome to Biopet
- (Bio Pipeline Execution Tool)
+###### (Bio Pipeline Execution Tool)
+
+## Introduction
+### System Requirements
+- Java 7 JVM
+- Maven 3 (does not need to be on shark)
+
+### Compiling Biopet
+
+1. Clone Biopet with `git clone git@git.lumc.nl:biopet/biopet.git`
+2. Go to Biopet directory
+3. run mvn_install_queue.sh, this install queue jars into the local maven repository
+4. run `mvn verify` to compile and package or do `mvn install` to install the jars also in local maven repository
+
+### Running a pipeline
+- Help: `java -jar Biopet(version).jar (pipeline of interest) -h`
+- Local: `java -jar Biopet(version).jar (pipeline of interest) (pipeline options) -run`
+- Shark: `java -jar Biopet(version).jar (pipeline of interest) (pipeline options) -qsub -jobParaEnv BWA -run`
+- DryRun: `java -jar Biopet(version).jar (pipeline of interest) (pipeline options)` 
+- DryRun(shark): `java -jar Biopet(version).jar (pipeline of interest) (pipeline options) -qsub -jobParaEnv BWA`
+
+    - A dry run can be performed to see if the scheduling and creating of the pipelines jobs performs well. Nothing will be executed only the job commands are created. If this succeeds it's a good indication you actual run will be successful as well.
+    - Each pipeline can be found as an options inside the jar file Biopet[version].jar which is located in the target directory and can be started with `java -jar <pipelineJarFile>`
+
+### Running a tool
+
+
+### Pipelines
+
+- [Flexiprep](https://git.lumc.nl/biopet/biopet/wikis/Flexiprep-Pipeline)
+- [Mapping](https://git.lumc.nl/biopet/biopet/wikis/Mapping-Pipeline)
+- [Gatk Variantcalling](https://git.lumc.nl/biopet/biopet/wikis/GATK-Variantcalling-Pipeline)
+- BamMetrics
+- Basty
+- GatkBenchmarkGenotyping
+- GatkGenotyping
+- GatkPipeline
+- GatkVariantRecalibration
+- GatkVcfSampleCompare
+- Gentrap (Under development)
+- Sage
+- Yamsvp (Under development)
+
+__Note that each pipeline needs a config file written in JSON format__
+
+- More info can be found here: [How To! Config](https://git.lumc.nl/biopet/biopet/wikis/Config)
 
 ## About 
-Go to the [about page](/about)
+Go to the [about page](about)
+
+## License
+
+See: [License](license)
diff --git a/docs/license.md b/docs/license.md
index 1695589bb..dc2b5e873 100644
--- a/docs/license.md
+++ b/docs/license.md
@@ -1,5 +1,4 @@
-
-    Copyright [2013-2014] [Sequence Analysis Support Core]
+    Copyright [2013-2014] [Sequence Analysis Support Core](https://sasc.lumc.nl/)
 
     Licensed under the Apache License, Version 2.0 (the "License");
     you may not use this file except in compliance with the License.
-- 
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