Laniakea Documentation

Laniakea provides the possibility to automate the creation of Galaxy-based virtualized environments through an easy setup procedure, providing an on-demand workspace ready to be used by life scientists and bioinformaticians.

Galaxy is a workflow manager adopted in many life science research environments in order to facilitate the interaction with bioinformatics tools and the handling of large quantities of biological data.

Once deployed each Galaxy instance will be fully customizable with tools and reference data and running in an insulated environment, thus providing a suitable platform for research, training and even clinical scenarios involving sensible data. Sensitive data requires the development and adoption of technologies and policies for data access, including e.g. a robust user authentication platform.

For more information on the Galaxy Project, please visit the https://galaxyproject.org

Laniakea has been developed by ELIXIR-IIB, the italian node of ELIXIR, within the INDIGO-DataCloud project (H2020-EINFRA-2014-2) which aims to develop PaaS based cloud solutions for e-science.

Note

Laniakea is in fast development. For this reason the code and the documentation may not always be in sync. We try to make our best to have good documentatation

Introduction

• Overview
• Service architecture
• ELIXIR-IIB: The Italian Infrastructure for Bioinformatics
• INDIGO-DataCloud
  • The ELIXIR-IIB use case in INDIGO
  • References

User documentation

• Launch Galaxy
  • Galaxy express
  • Galaxy live build
  • Instantiate Galaxy
  • Galaxy access
• Launch Galaxy Docker
  • Instantiate Galaxy
  • Galaxy access
  • References
• Launch Galaxy cluster
  • Galaxy cluster
  • Galaxy elastic cluster
  • Instantiate Galaxy
  • Galaxy access
• Manage an encrypted instance
  • Retrieve the encrypted storage passphrase
  • Restart Galaxy on an encrypted instance
  • Command line interface: luksctl
• Create SSH Keys
  • Create your SSH key with Laniakea
  • Remove the SSH key from Laniakea
  • How to create SSH keys on Linux or macOS
  • How to create SSH keys on Windows
• Virtual hardware presets
  • Laniakea@ReCaS
• Galaxy Flavours
  • Galaxy minimal
  • Galaxy CoVaCS
  • Galaxy GDC Somatic Variant
  • Galaxy RNA workbench
  • Galaxy Epigen
• Submit yout flavour
  • Tool list configuration options
  • Conda support
  • References
• Reference Data
  • data.galaxyproject.org
  • elixir-italy.covacs.refdata
  • elixir-italy.galaxy.refdata
  • Supplementary information
• Galaxy production environment
  • OS support
  • PostgresSQL
  • NGINX
  • uWSGI
  • Proftpd
  • Supervisord
  • Paths
  • Enable Dockerized tools support in job_conf.xml
• Galaxy Docker instance
  • Configuration files
  • CVMFS configuration
  • Galaxy docker usage
  • Galaxy Docker usage tutorial
• Cluster configuration
  • job_conf.xml configuration
  • Shared file system
  • Network configuration
  • Worker nodes SSH access
  • Worker nodes deployment on elastic cluster
  • References
• Authentication
  • Registration
  • Login
• Frequently Asked Questions
  • How to manually recover Galaxy after VM reboot
  • I’m unable to create users from admin panel

Admin documentation

• The encryption layer
  • The encryption strategy
  • Storage encryption workflow
  • File System Encryption Test
  • Fast-luks script
  • Luksctl: LUKS volumes management
  • LUKSctl: APIs
  • Cryptsetup hints
  • References
• Galaxyctl: Galaxy management
  • Galaxyctl basic usage
  • Logging
  • Advanced options
  • Configuration file
  • Features
• Laniakea Ansible Roles
  • indigo-dc.galaxycloud
  • indigo-dc.galaxycloud-os
  • indigo-dc.galaxycloud-tools
  • indigo-dc.galaxycloud-refdata
  • indigo-dc.galaxycloud-fastconfig
  • indigo-dc.galaxycloud_docker
  • indigo-dc.cvmfs-client
  • indigo-dc.cvmfs-server
• TOSCA templates
  • Custom types
  • Galaxy template
  • Galaxy cluster template
• Build CVMFS server for reference data
  • Create CernVM-FS Repository
  • Client configuration
  • Populate a CernVM-FS Repository (with reference data)
  • Reference data download
  • References
• Vault configuration
  • Vault main concepts
  • Vault authentication and authorization flow
  • Vault passphrase storage flow
  • Passphrase path on Vault
• Laniakea Dashboard
  • Configuration
• Laniakea installation
  • Services end-points
  • Service installation

GitHub repository

https://github.com/Laniakea-elixir-it

DockerHub repository

https://hub.docker.com/r/laniakeacloud

Support

If you need support please contact us to: laniakea.helpdesk@gmail.com

Software glitches and bugs can occasionally be encoutered. The best way to report a bug is to open an issue on our GitHub repository.

Cite

Marco Antonio Tangaro, Giacinto Donvito, Marica Antonacci, Matteo Chiara, Pietro Mandreoli, Graziano Pesole, Federico Zambelli, Laniakea: an open solution to provide Galaxy “on-demand” instances over heterogeneous cloud infrastructures, GigaScience, Volume 9, Issue 4, April 2020, giaa033, https://doi.org/10.1093/gigascience/giaa033

Tha paper is available here.

Licence

As an open source project Laniakea is made up of many pieces of software created by a range of individuals, teams, and companies. Laniakea is a collective work, and each piece of software within this work has its own license.

Your use of each piece of software is governed by the terms of its accompanying license. Redistribution of parts or the whole of Laniakea may require you to comply with additional license requirements.

Galaxy tutorials

Galaxy training network: https://galaxyproject.org/teach/gtn/

Galaxy For Developers: https://crs4.github.io/Galaxy4Developers/

Indices and tables

• Index
• Module Index
• Search Page