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
• TransparentMultiHopSSH? - How to connect via the proxy

Documentation on the MOLGENIS software suite

• MOLGENIS OMX applications SOPs
  • SopMolgenis? - How to check out and build a MOLGENIS app
  • OMX Manual?
  • SopMolgenisRelease? - How to create a MOLGENIS release
• MOLGENIS framework
  • Developer Manual
• xQTL workbench
  • using xQTL workbench for multi-level QTL mapping
• MOLGENIS/compute SOPs
  • 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

• Molgenis Servers? - List of all VMs in our cloud.
• Create Molgenis VM - How to request and configure a new Molgenis VM cloned from the 'molgenis gold' template.
• Install SOP / Tomcat7 - How to deploy Tomcat7 on a Molgenis VM.
• Install SOP / Tomcat Auth - How to add Tomcat 7 basic login authentication.
• MySQL setup?
• Install SOP / Deploy MOLGENIS via Jenkins - How to deploy MOLGENIS on a VM using Jenkins]
• SOP Nightlies? - How to create a nightly build

GCC HPC cluster + SFTP server

• For Users:
  • Storage SOP Users? - What is stored where
  • Analyses SOP Users? - How to manage your jobs on the GCC cluster
• For Admins:
  • SOP New User - Creating a new user account for the HPC infrastructure
  • SOP Deploy Tools and Resources - Installation/deployment of tools and resources.
  • Storage Config - Details on storage for GCC cluster + SFTP server.
  • Cluster Config - Configuration details of the GCC cluster

New employee

• SOP new Employee (employee) - Manual for employee
• SOP New Employee (team) - Manual for team
• IntellijTips - Tips for using IntelliJ

Documentation for specific projects / groups

Internal GCC SOPs

• How to print the scrum cards
• Connect to Xerox printers for Mac OS X
• SOPs - Most used Standard Operating Procedures (authorized users only)
• Intranet - List of all SOPs; common and obscure (authorized users only)

IBD SOP

• 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)