Howto

Beacon Installation and Deployment

An open-access online tutorial How to install and deploy Beacon has been launched on the ELIXIR-SI eLearning Platform (EeLP). Learning materials are provided by ELIXIR Beacon project contributors from Finland and Spain.

The tutorial is registered on ELIXIR Training eSupport System (TeSS) and contains instructions for Beacon installation and deployment, both as instruction manual and tutorial video. No username and password is required to access the tutorial.

@markowhatever 2019-03-26: more ...

FAQ - Precise Variants

Precise variants are such with annotated sequences of 0….n length, and bases of [ATCGN] for the referenceBases and alternateBases attributes (N for “not specified”).

@mbaudis 2018-10-17: more ...

Genome Coordinate use for Beacon Queries

The coordinate system that should be used throughout GA4GH standards is 0-based half open.

@mbaudis 2019-03-14: more ...

ProgenetixTemplate::bootstrap_site.pl Perl Code Documentation

2019-07-10: more ...

ProgenetixTemplate::podmd.pl Perl Code Documentation

2019-07-10: more ...

Range Queries and Structural Variants

The adoption of

  • variantType
  • startMin, startMax
  • endMin, endMax

into the Beacon v0.4 release enabled the execution of

  • range queries
  • fuzzy position matching
  • arbitrary sequence variants (though limited through supported & documented vocabularies)

@mbaudis 2018-10-17: more ...

Website - Add and Edit Pages

New pages are added to the website inside one of the “collections” directories in the / directory. This can either be done by adding files locally or on Github (if hosted there).

@mbaudis 2019-03-25: more ...

Website - Directories and Files

The Progenetix Jekyll template modifies the standard Jekyll file structure.

@mbaudis 2019-03-14: more ...

Website - Header for Web Pages

The YAML headers are necessary to process the Markdown (or HTML) files in the page collections. The Progenetix Jekyll template uses standard Jekyll headers, but also adds some additional parameters.

@mbaudis 2019-03-14: more ...

Local Jekyll based website generation

In an ideal scenario, your Github served website could be build locally, with the same output structure and layout.

@mbaudis 2019-03-14: more ...