[[TOC()]]

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

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

== Documentation on the MOLGENIS software suite ==
 * [wiki:MolgenisGuide Developer Manual] - OUTDATED in progress of migration to github
 * [wiki:xQTL using xQTL workbench for multi-level QTL mapping]

== Documentation on the MOLGENIS/compute ==
 * [wiki:ComputeStart MOLGENIS/compute Start page] featuring code, manuals and presentations.
 * DeployDependencies - How to deploy tools and resources for your workflows on different backends (Grid, PBS cluster, etc.)

== GCC Cloud VMs / Jenkins / Tomcat / MySQL ==
 * [wiki:MolgenisServers Molgenis Servers] - List of all VMs in our cloud.
 * [wiki:GccSopCreateMolgenisVM Create Molgenis VM] - How to request and configure a new Molgenis VM cloned from the 'molgenis gold' template.
 * [wiki:GccSopInstallationTomcat7 Install SOP / Tomcat7] - How to deploy Tomcat7 on a Molgenis VM.
 * [wiki:GccSopInstallationTomcat7AddAuthentication Install SOP / Tomcat Auth] - How to add Tomcat 7 basic login authentication.
 * [wiki:GccSopInstallationDeployServerInJenkins Install SOP / Deploy MOLGENIS via Jenkins] - How to deploy MOLGENIS on a VM using Jenkins.
 * [wiki:MysqlSetup MySQL setup]
 * [wiki:SopNightlyBuild SOP Nightlies] - How to create a nightly build

== 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

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

= 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)
 * GccSopMolgenisRelease - How to create a MOLGENIS release
 * GccSopSystemsGeneticsRelease - How to create a Systems Genetics release

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

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

== BBMRI SOPs ==
 * SopUpdateBbmriApp - How to Update BBMRIApp (Legacy SOP)

== Liferay Molgenis SOPs ==
 * [wiki:SOPConfigureLiferay] - How to Configure Liferay including Molgenis (SOP)

== ASE SOP ==
 * [wiki:GCCSopAseDeploy] - How to deploy the ASE site

== PALGA SOP ==
 * [wiki:GCCSopPALGADeploy] - How to deploy PALGA