Documentation

Welcome to documentation on the MOLGENIS software suite.

Internal

• Standard Operating Procedures (authorized users only)

Molgenis OMX applications SOPs

• SopMolgenis? - how to check out and build a molgenis app
• SopUseJQuerytree - how to find, instantiate and use
• Omx manual?
• how to do a molgenis release?

Servers / VMs / Jenkins / Tomcat

• MolgenisServers? - listing of MOLGENIS servers
• ​How to deploy Tomcat7
• ​Deploy server in Jenkins 
• Create Molgenis VM? - How to request and configure a new copy of 'molgenis gold'
• SopNightlyBuild? - how to create a nightly build
• Mysql setup?

Legacy SOPs

• SopUpdateBbmriApp - How to Update Bbmri App

Handy SOPs

• How to print the scrum cards
• ​ConnectToXeroxPrintersForMac

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)

Software

• MOLGENIS framework
  • Developer Manual
• xQTL workbench
  • 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.)