home.md

 # Welcome to Wiki Shark cluster
 ## Introduction
-In this wiki, we will introduce the Shark cluster. We assume you know your way around in the terminal and that you will use the cluster in a responsible way and respect the available resources. Remember that a cluster runs many different processes submitted by many different users. If you are not sure what you are doing, ask your administrator before submitting very intensive jobs! For more examples and useful commands you can use our [gitlab repository](git@git.lumc.nl:shark/SHARK.git)
+In this wiki, we will introduce the Shark cluster. We assume you know your way around in the terminal and that you will use the cluster in a responsible way and respect the available resources. Remember that a cluster runs many different processes submitted by many different users. If you are not sure what you are doing, ask your administrator before submitting very intensive jobs! For more examples and useful commands you can use our [gitlab repository](git@git.lumc.nl:shark/SHARK.git).
 
 Shark cluster runs with [Open Grid Scheduler/Grid Engine](http://gridscheduler.sourceforge.net/) this  is a free and open-source batch-queuing system for distributed resource management. OGS/GE is based on Sun Grid Engine, and maintained by the same group of external (i.e. non-Sun) developers who started contributing code to Sun Grid Engine since 2001. 
 
@@ -11,8 +11,8 @@ The following links contain the minimal information you need to get started on t
 When using the cluster you acknowledge that you have read and understand the following articles.
 
  * [Guidelines](Guidelines) -- what you can and can't do on this cluster
- * [function of the Shark cluster](Primairy) -- Primary usage Shark cluster
- * [network shares](Network_shares) -- where to put your data
+ * [Function of the Shark cluster](Primairy) -- Primary usage Shark cluster
+ * [Network shares](Network_shares) -- where to put your data
  * [Queues](Queues) -- which queue is for what
  * [Batch queuing commands](qsubCommands) -- explanation of the qsub command
  * [Examples](Examples) -- examples how to qsub your jobs
@@ -20,11 +20,10 @@ When using the cluster you acknowledge that you have read and understand the fol
  * [SGE state symbol codes](StateCode) -- Sun Grid Engine SGE state letter symbol codes meanings
  * [FAQ](FAQ) -- Frequently asked questions and answers
  * [Presentations](Presentations) -- Interesting presentations
- * [testsets](testsets) -- Featured test data
- * [Using the checkpointing queue](CheckpointingQueue) -- how/when to use the checkpointing queue
-
+ * [Testsets](testsets) -- Featured test data
+ 
 ## Configuration Shark cluster
- * [configuration Type of headnode and blade servers](Configuration)
+ * [Configuration Type of headnode and blade servers](Configuration)
  * [Graphical representation of the shark cluster](Graphicalview)
  * [Description of the execute nodes](DescriptionExenode)
  * [Hardware ownership](HardwareOwnership)
@@ -58,7 +57,7 @@ When using the cluster you acknowledge that you have read and understand the fol
  * [Contact Information](Contact_info_shark)
  * [Ganglia Shark cluster monitor](http://shark.lumcnet.prod.intern/ganglia/?c=Shark%20Cluster&m=load_one&r=hour&s=descending&hc=4&mc=2) -- view the load, disk space etc. on the Shark cluster
  * [Grid Engine HOWTOs](http://arc.liv.ac.uk/SGE/howto/).
- * [SVN repository (for course material and example scripts).](https://humgenprojects.lumc.nl/svn/shark/)
+ * [Gitlab repository (for course material and example scripts).](git@git.lumc.nl:shark/SHARK.git)
 
 ## Usage Statistics
  * [Shark Usage 2012](http://shark.lumcnet.prod.intern/stats/SharkStats2012.html)