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

Servers (VMs) / Jenkins / Tomcat / MySQL

• MolgenisServers? - 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.
• SopInstallationTomcat7? - How to deploy Tomcat7 on a Molgenis VM.
• How to add Tomcat 7 basic login authentication?
• MySQL setup?
• Deploy server in Jenkins? 
• SopNightlyBuild? - How to create a nightly build

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.)

New employee

• SOP new Employee (employee) - Manual for employee
• SOP New Employee (team) - Manual for team

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
  • Storage Config - Details on storage for GCC cluster + SFTP server. Includes instructions for installation/deployment of tools and resources.
  • Cluster Config - Configuration details of the GCC cluster

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)