Merge branch 'readme-fixes' of git://github.com/martijnvermaat/biopet into...

Merge branch 'readme-fixes' of git://github.com/martijnvermaat/biopet into martijnvermaat-readme-fixes

README.md

@@ -46,7 +46,7 @@ If the dry run proceeds without problems, you can then do the real run by using
 $ biopet pipeline <pipeline_name> -config <path/to/config.json> -qsub -jobParaEnv BWA -retry 2 -run
 ~~~
 
-It is usually a good idea to do the real run using `screen` or `nohup` to prevent the job from terminating when you log out of SHARK. In practice, using `biopet` as it is is also fine. What you need to keep in mind, is that each pipeline has their own expected config layout. You can check out more about the general structure of our config files [here](general/config.md). For the specific structure that each pipeline accepts, please consult the respective pipeline page.
+It is usually a good idea to do the real run using `screen` or `nohup` to prevent the job from terminating when you log out of SHARK. In practice, using `biopet` as it is is also fine. What you need to keep in mind, is that each pipeline has their own expected config layout. You can check out more about the general structure of our config files [here](docs/config.md). For the specific structure that each pipeline accepts, please consult the respective pipeline page.
 
 ### Running Biopet in your own computer
 
@@ -57,7 +57,7 @@ At the moment, we do not provide links to download the Biopet package. If you ar
 
 Biopet is based on the Queue framework developed by the Broad Institute as part of their Genome Analysis Toolkit (GATK) framework. The current Biopet release is based on the GATK 3.3 release.
 
-We welcome any kind of contribution, be it merge requests on the code base, documentation updates, or any kinds of other fixes! The main language we use is Scala, though the repository also contains a small bit of Python and R. Our main code repository is located at [https://git.lumc.nl/biopet/biopet](https://git.lumc.nl/biopet/biopet/issues), along with our issue tracker.
+We welcome any kind of contribution, be it merge requests on the code base, documentation updates, or any kinds of other fixes! The main language we use is Scala, though the repository also contains a small bit of Python and R. Our main code repository is located at [https://github.com/biopet/biopet](https://github.com/biopet/biopet/issues), along with our issue tracker.
 
 ## Local development setup
 
@@ -73,7 +73,7 @@ $ mvn -U clean install
 This will install all the required dependencies to your local maven repository. After this is done, you can clone our repository and test if everything builds fine:
 
 ~~~
-$ git clone git@git.lumc.nl:biopet/biopet.git
+$ git clone https://github.com/biopet/biopet.git
 $ cd biopet
 $ mvn -U clean install
 ~~~
@@ -83,8 +83,8 @@ If everything builds fine, you're good to go! Otherwise, don't hesitate to conta
 
 ## About
 
-Go to the [about page](about)
+Go to the [about page](docs/about.md)
 
 ## License
 
-See: [License](license.md)
+See: [License](docs/license.md)