[[TOC()]]

Project / group specific documentation at the bottom of this page...

= Documentation relevant for multiple groups / projects =

 * [wiki:RequestAccount] - How to request an account for access to GCC maintained infrastructure
 * [wiki:DataSharing] - How to up-/download data via SFTP
 * [wiki:TransparentMultiHopSSH] - How to connect via the proxy

== Servers (VMs) / Jenkins / Tomcat / MySQL ==
 * [wiki:MolgenisServers] - List of all VMs in our cloud.
 * [wiki:SopCreateMolgenisVM Create Molgenis VM] - How to request and configure a new Molgenis VM cloned from the 'molgenis gold' template.
 * [wiki:SopInstallationTomcat7] - How to deploy Tomcat7 on a Molgenis VM.
 * [[SopInstallationTomcat7AddAuthentication| How to add Tomcat 7 basic login authentication]]
 * [wiki:MysqlSetup MySQL setup]
 * [wiki:SopInstallationDeployServerInJenkins#SopInstallationDeployServerInJenkins Deploy server in Jenkins] 
 * [wiki:SopNightlyBuild] - How to create a nightly build

== Documentation on the MOLGENIS software suite ==
 * MOLGENIS OMX applications SOPs
   * [wiki:SopMolgenis] - How to check out and build a MOLGENIS app
   * [wiki:omxManual OMX Manual]
   * [wiki:SopMolgenisRelease] - How to create a MOLGENIS release
 * MOLGENIS framework
   * [wiki:MolgenisGuide Developer Manual]
 * xQTL workbench
   * [wiki:xQTL using xQTL workbench for multi-level QTL mapping]
 * MOLGENIS/compute SOPs
   * [wiki:ComputeStart MOLGENIS/compute Start page] featuring code, manuals and presentations.
   * [wiki:DeployDependencies] - How to deploy tools and resources for your workflows on different backends (Grid, PBS cluster, etc.)

== New employee ==
 * [wiki:GCCSopNewEmployee SOP new Employee (employee)] - Manual for employee
 * [wiki:GCCSopNewEmployeeGCC SOP New Employee (team)] - Manual for team

== GCC HPC cluster + SFTP server ==
 * For Users:
   * [wiki:SopUseGccStorage Storage SOP Users] - What is stored where
   * [wiki:SopUseGccCluster Analyses SOP Users] - How to manage your jobs on the GCC cluster
 * For Admins:
   * [wiki:GccSopNewUser SOP New User] - Creating a new user account for the HPC infrastructure
   * [wiki:GccSopDeployToolsAndResources SOP Deploy Tools and Resources] - Installation/deployment of tools and resources.
   * [wiki:GccStorage Storage Config] - Details on storage for GCC cluster + SFTP server.
   * [wiki:GccCluster Cluster Config] - Configuration details of the GCC cluster

= Documentation for specific projects / groups =

== Internal GCC SOPs ==
 * [wiki:SopPrintScrum How to print the scrum cards]
 * [wiki:ConnectToXeroxPrintersForMac Connect to Xerox printers for Mac OS X]
 * [wiki:GccOperatingProcedures SOPs] - Most used Standard Operating Procedures (authorized users only)
 * [wiki:GccIntranet Intranet] - List of all SOPs; common and obscure (authorized users only)

== IBD SOP ==
 * [wiki:GCCSopConvertIBDStageData Retreive and convert IBD Stage data]

== LifeLines SOPs ==
 * [wiki:SopConvertLifeLinesGenoData] - how to prepare the geno data from release 3 + imputation (2 sets)

== BBMRI SOPs ==
 * [wiki:SopUpdateBbmriApp] - How to Update BBMRIApp (Legacy SOP)