Documentation

Welcome to documentation on the MOLGENIS software suite.

Software

• MOLGENIS framework
  • Developer Manual
• xQTL workbench
  • using xQTL workbench for multi-level QTL mapping

Internal

• 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
• ​How to deploy Tomcat7
• ​Deploy server in Hudson
• 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
• 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
• Mysql setup?
• How to print the scrum cards
• [omxManual Omx manual]

Using the GCC compute cluster

• SOP Users? - How to use the GCC cluster
• SOP New User - Creating a new user account for the GCC infrastructure
• 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:

• ​JQGridPluginProtocol - how to use the Tuple Table viewer

• ​ConnectToXeroxPrintersForMac

MOLGENIS/compute SOPs

• DeployDependencies? - How to deploy tools and resources for your workflows on different backends (Grid, PBS cluster, etc.)