Initial documentation using mkdocs, #38 user documentation

docs/about.md

+# About biopet
+
+## The philosophy
+
+We develop tools and pipelines for several purposes in analysis. Most of them 
+share the same methods. So the basic idea is to let them work on the same 
+platform and reduce code duplication and increase maintainability.
+
+## Compute Cluster support
+
+
+## The Team
+
+
+## Contact
+
+We even have a website: https://sasc.lumc.nl/
\ No newline at end of file

docs/cluster/oge.md

+# Introduction
+
+
+
+# Sun Grid Engine
+
+
+
+# Open Grid Engine
\ No newline at end of file

docs/index.md

+# Welcome to Biopet
+ (Bio Pipeline Execution Tool)
+
+## About 
+Go to the [about page](/about)

docs/license.md

+
+    Copyright [2013-2014] [Sequence Analysis Support Core]
+
+    Licensed under the Apache License, Version 2.0 (the "License");
+    you may not use this file except in compliance with the License.
+    You may obtain a copy of the License at
+
+        http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing, software
+    distributed under the License is distributed on an "AS IS" BASIS,
+    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+    See the License for the specific language governing permissions and
+    limitations under the License.
\ No newline at end of file

docs/pipelines/basty.md

+# Introduction
+
+# Invocation
+
+# Example
+
+# Testcase A
+
+# Testcase B
+
+# Examine results
+
+## Result files
+
+## Best practice
+
+# References

docs/pipelines/flexiprep.md

+# Introduction
+
+# Invocation
+
+# Example
+
+# Testcase A
+
+# Testcase B
+
+# Examine results
+
+## Result files
+
+## Best practice
+
+# References

docs/pipelines/gentrap.md

+# Introduction
+
+# Invocation
+
+# Example
+
+# Testcase A
+
+# Testcase B
+
+# Examine results
+
+## Result files
+
+## Best practice
+
+# References

docs/pipelines/mapping.md

+# Introduction
+
+# Invocation
+
+# Example
+
+# Testcase A
+
+# Testcase B
+
+# Examine results
+
+## Result files
+
+## Best practice
+
+# References

docs/pipelines/sage.md

+# Introduction
+
+# Invocation
+
+# Example
+
+# Testcase A
+
+# Testcase B
+
+# Examine results
+
+## Result files
+
+## Best practice
+
+# References

docs/pipelines/yamsvp.md

+# Introduction
+
+# Invocation
+
+# Example
+
+# Testcase A
+
+# Testcase B
+
+# Examine results
+
+## Result files
+
+## Best practice
+
+# References

mkdocs.yml

+site_name: Biopet
+pages:
+- ['index.md', 'Home']
+- ['pipelines/basty.md', 'Pipelines', 'Basty']
+- ['pipelines/flexiprep.md', 'Pipelines', 'Flexiprep']
+- ['pipelines/gentrap.md', 'Pipelines', 'Gentrap']
+- ['pipelines/mapping.md', 'Pipelines', 'Mapping']
+- ['pipelines/sage.md', 'Pipelines', 'Sage']
+- ['pipelines/yamsvp.md', 'Pipelines', 'Yamsvp']
+- ['cluster/oge.md', 'OpenGridEngine']
+- ['about.md', 'About']
+- ['license.md', 'License']
+theme: readthedocs
+repo_url: https://git.lumc.nl/biopet/biopet