[[TOC()]] = Documentation = Welcome to documentation on the MOLGENIS software suite. == Internal == * [wiki:GccOperatingProcedures Standard Operating Procedures (authorized users only)] == Molgenis OMX applications SOPs == * SopMolgenis - how to check out and build a molgenis app * [wiki:SopUseJQuerytree] - how to find, instantiate and use * [wiki:omxManual Omx manual] * [wiki:SopMolgenisRelease how to do a molgenis release] === Servers / VMs / Jenkins / Tomcat === * 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' * SopNightlyBuild - how to create a nightly build * [wiki:MysqlSetup Mysql setup] == Legacy SOPs == * SopUpdateBbmriApp - How to Update Bbmri App == Handy SOPs == * [wiki:SopPrintScrum How to print the scrum cards] * [http://www.molgenis.org/wiki/ConnectToXeroxPrintersForMac ConnectToXeroxPrintersForMac] == 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] == Software == * '''MOLGENIS framework''' * [wiki:MolgenisGuide Developer Manual] * '''xQTL workbench''' * [wiki:xQTL using xQTL workbench for multi-level QTL mapping] == MOLGENIS/compute SOPs == * DeployDependencies - How to deploy tools and resources for your workflows on different backends (Grid, PBS cluster, etc.)