Documentation relevant for all groups / projects / infra

• RequestAccount? - How to request an account for access to GCC maintained infrastructure (Cloud & HPC clusters)
• DataSharing? - How to up-/download data via SFTP
• TransparentMultiHopSSH? - How to connect via the proxy

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

How to compute on the Calculon, Boxy, Zinc-Finger and Leucine-Zipper Clusters.

• Overview? - Description of the different HPC environments

For Users

• Getting access? - How to request an account.
• Available resources? - What is available and where.
• Login? - How to start a session.
• Storage SOP? - What is stored where.
• Analyses SOP? - How to manage your jobs on the cluster.
• Support? - FAQs, mailinglists, courses and contact info to get in touch with an admin.
• Scheduled Maintenance? - Policy and dates for scheduled maintenance.

For Admins

• SOP Accounts? - Managing users and groups for the HPC infrastructure.
• Deploy Apps & Data - SOP for central deployment of software and reference data sets.
• Shared Storage Config? - How are logical file systems related to physical ones.
• Compute Config? - SLURM schedulers, partitions and nodes.

Documentation for 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• Developer Manual - OUTDATED in progress of migration to github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
• Using Molgenis-connect - How to deploy Molgenis-connect in tomcat 7

Documentation for the MOLGENIS/compute script generator

• MOLGENIS/compute Start page featuring code, manuals and presentations.

Documentation for specific projects / groups

Internal GCC SOPs

• SOP new Employee (employee) - Manual for employee
• SOP New Employee (team) - Manual for team
• 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
• GccSopMolgenisComputeRelease - How to create a MOLGENIS Compute release

IBD SOP

• Retreive and convert IBD Stage data

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