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Table of Contents
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
- Developer Manual - OUTDATED in progress of migration to github
- using xQTL workbench for multi-level QTL mapping
- Tracking Code - Add app statistics tracking code
- Using SORTA - How to deploy SORTA in tomcat 7
Documentation on the MOLGENIS/compute
- 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 / WordPress
- 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.
- Install SOP / Deploy MOLGENIS via Jenkins - How to deploy MOLGENIS on a VM using Jenkins.
- Molgenis VM multiple certificates - Use Molgenis VM with multiple certificates.
- MySQL setup?
- SOP Nightlies? - How to create a nightly build
- SOP WordPress - How to manage WordPress websites
High Performance Computing (HPC) infra
- version 1.x (Deprecated) - The GCC cluster
- version 2.x (New!) - The Calculon, Zinc-Finger and Leucine-Zipper Clusters
- Overview? - Description of the differences between the 1.x and 2.x HPC environments
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)
- GccSopMolgenisRelease - How to create a MOLGENIS release
- GccSopSystemsGeneticsRelease - How to create a Systems Genetics release
IBD SOP
LifeLines SOPs
- SopConvertLifeLinesGenoData - how to prepare the geno data from release 3 + imputation (2 sets)
- GccSopLifelinesDeploy - How to deploy Lifelines
BBMRI SOPs
- SopUpdateBbmriApp - How to Update BBMRIApp (Legacy SOP)
Liferay SOPs
- GccSopLiferayBBMRI_NL - How to configure and install Liferay (SOP)
ASE SOP
- GccSopAseDeploy - How to deploy the ASE site
PALGA SOP
- GccSopPALGADeploy - How to deploy PALGA
PhD roadmap
- GccPhdChao - Chao`s roadmap and corresponding stories