West-Life Virtual Research Environment Docs
  • Introduction
  • Data Management
  • Virtual Folder
    • User's guide
      • Settings
        • Import settings from another Virtual Folder
      • File Manager
      • File Picker
      • Related applications
        • Jupyter notebook
      • Metadata
    • Installation guide
      • Cloud installation
      • Local installation
      • Integration with SSO
    • Integration guide
      • Select File or Dir from Virtual Folder
      • Working with WEBDAV
      • Embedding Virtual Folder Component
      • Adding component into Virtual Folder
    • Developer's guide
      • Backend
      • Frontend - Web Application
      • Metadata and API
        • Dataset metadata and API
        • File metadata and API
      • Import Export Settings API
      • Related application and services
      • Untitled
  • Virtual Machines and Containers
    • Preparing vagrant VM template
    • Preparing docker container
  • Repository
    • Installation guide
      • Prerequisites
      • Automatic installation
      • Manual installation from source codes
    • User's guide
      • Scientist imports project proposal
      • Staff uploads data
      • Scientist works with dataset
      • Metadata
    • Developer's guide
      • Metadata generation
      • ARIA integration
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  • Jupyter binary installation
  • Jupyter local installation
  • Jupyter manual installation
  1. Virtual Folder
  2. Developer's guide

Related application and services

Virtual folder can be installed with optional software, application and services.

Jupyter binary installation

You may use binary installation from /cvmfs/west-life.egi.eu repository, to do that, create link /opt/jupyter to e.g. the latest version:

ln -s /cvmfs/west-life.egi.eu/software/jupyter/latest /opt/jupyter

Then enable the jupyter tasks in metadata service configuration /etc/systemd/system/westlife-metadata.service by adding VF_ALLOW_LAB=true VF_ALLOW_NOTEBOOK=true. See Manual configuration for details.

Jupyter local installation

In order to install Jupyter in local installation during bootstrap of VF - set local variable ALLOW_JUPYTER=1before launching bootstrap, i.e.:

# define where VF sources are located 
# export WP6SRC=/vagrant
export ALLOW_JUPYTER=1 # enable jupyter
$WP6SRC/bootstrap/bootstrap.sh

Jupyter manual installation

Jupyter notebook and Jupyter Lab can be installed manually, see/edit the bootstrap/bootstrapJupyter.sh and set local variable ALLOW_JUPYTER=1before launching this script:

# define where VF sources are located 
# export WP6SRC=/vagrant
export ALLOW_JUPYTER=1 # enable jupyter
$WP6SRC/bootstrap/bootstrapJupyter.sh

Python environment with jupyter and all other dependencies will be installed by default at /opt/jupyter path. You need then to enable tasks in virtual folder UI:

  • enable jupyter notebook and jupyter lab task in metadata service configuration /etc/systemd/system/westlife-metadata.service by adding VF_ALLOW_LAB=true VF_ALLOW_NOTEBOOK=true:

    [Service]
    ...
    Environment=VF_ALLOW_LAB=true
    Environment=VF_ALLOW_NOTEBOOK=true
    ...

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Last updated 6 years ago