[[TOC()]]

= Documentation =
Welcome to documentation on the MOLGENIS software suite.

== Software ==
 * '''MOLGENIS framework'''
   * [wiki:MolgenisGuide Developer Manual]
 * '''xQTL workbench'''
   * [wiki:xQTL using xQTL workbench for multi-level QTL mapping]

== Internal ==
 * [wiki:GccOperatingProcedures Standard Operating Procedures (authorized users only)]

= All our standard operation procedures =
See MolgenisAppStories for requirements.

== Molgenis Apps deployment SOPs ==
Stories that hold for any 'app':

 * MolgenisServers - listing of MOLGENIS servers
 * [http://www.molgenis.org/wiki/SopInstallationTomcat7#SopInstallationTomcat7 How to deploy Tomcat7]
 * [http://www.molgenis.org/wiki/SopInstallationDeployServerInJenkins#SopInstallationDeployServerInJenkins Deploy server in Jenkins] 
 * [wiki:SopCreateMolgenisVM Create Molgenis VM] - How to request and configure a new copy of 'molgenis gold'
 * SopDeployMolgenisApps - how to automatically check-out, build and run one of the molgenis_apps
 * SopMolgenis - how to check out and build a molgenis app
 * SopLoadData - how to load data into your app install
 * [wiki:SopUseJQuerytree] - how to find, instantiate and use
 * SopGenericImporter - how to use, how to import, how the interface works
 * SopNightlyBuild - how to create a nightly build
 * SopUseGenericImporter - how to use GenericImporter
 * SopUpdateBbmriApp - How to Update Bbmri App
 * [wiki:MysqlSetup Mysql setup]
 * [wiki:SopPrintScrum How to print the scrum cards]
 * [omxManual Omx manual]
 * [wiki:SopMolgenisRelease how to do a molgenis release]

== Using the GCC compute cluster ==
 * [wiki:SopUseGccCluster SOP Users] - How to use the GCC cluster
 * [wiki:GccSopNewUser SOP New User] - Creating a new user account for the GCC infrastructure
 * [wiki:GccCluster SOP Admins] - Configuration details of the GCC cluster

== LifeLines Research portal deployment SOPs ==
Depends on above. Specific stories for LifeLines data:

 * SopConvertLifeLinesGenoData - how to prepare the geno data from release 3 + imputation (2 sets)
 * SopConvertLifeLinesPhenoData - how to load the database release
 * SopLinkVmToWom - how to link the virtual machine to the WOA
 * GccLifeLinesSopDeployPortal - how to deploy the Research Portal on a VM

== LifeLines user manuals ==
 * HelpUsingMatrix - How to select Measurements and filter matrix
 * HelpDownloadPlink - How to download PLINK ready files (TFAM, TPED)

== !TupleTable SOPs ==
Depends on above. Specific stories for LifeLines data:

 * [http://www.molgenis.org/wiki/GccTupleTable JQGridPluginProtocol] - how to use the Tuple Table viewer

 * [http://www.molgenis.org/wiki/ConnectToXeroxPrintersForMac ConnectToXeroxPrintersForMac]

== MOLGENIS/compute SOPs ==
 * DeployDependencies - How to deploy tools and resources for your workflows on different backends (Grid, PBS cluster, etc.)