Reference Data

Many Galaxy tools rely on the presence of reference data, such as alignment indexes or reference genome sequences, to efficiently work. A complete set of Reference Data, able to work with most common tools for NGS analysis is available for each Galaxy instance deployed.

The reference data are available for many species and shared among all the instances, avoiding unnecessary and costly data duplication, exploiting a CernVM-FS (CVMFS) repository.

Laniakea automatically configures Galaxy to properly use them.

By default Laniakea exploits the usegalaxy.org reference data, but for specific needs, e.g. new tools, it is possible to enable, using the Laniakea Dahsobard, different repositories:

Reference data indexes available for bowite

`data.galaxyproject.org`

Description:

The usegalaxy.org CVMFS repository hosts more than 4 TB of reference data. There are two primary directories in the reference data repository:

/managed: Data generated with Galaxy Data Managers, organized by data table (index format), then by genome build.
/byhand: Data generated prior to the existence/use of Data Managers, manually curated.

Currently, the Laniakea instances are preconfigured to mount /byhand data. More information can be found here.

For GDC Somatic Variant flavour (GDC Somatic Variant on Galaxy) Galaxy is configured to use also an additional gdc_tool_data_table_conf.xml, which can be found here.

`elixir-italy.covacs.refdata`

Description:: This repository hosts specific reference data for CoVaCS pipeline, Laniakea configure the CoVaCS flavours to consume these data.

Reference data cvmfs	Details
cvmfs repository name	elixir-italy.covacs.refdata
cvmfs server url	90.147.75.251
cvmfs config file	elixir-italy.covacs.refdata.conf
cvmfs key file	elixir-italy.covacs.refdata.pub
cvmfs proxy url	DIRECT
galaxy tool data table	tool-data-table.xml

`elixir-italy.galaxy.refdata`

Description:: This repository is recommended only for testing tools and is currently not available on the Laniakea Dashboard. It is used for those tools need to ship reference data still not in the Galaxy Official CVMFS.

Reference data cvmfs	Details
cvmfs repository name	elixir-italy.galaxy.refdata
cvmfs server url	90.147.102.186
cvmfs config file	elixir-italy.galaxy.refdata.conf
cvmfs key file	elixir-italy.galaxy.refdata.pub
cvmfs proxy url	DIRECT
galaxy tool data table	tool-data-table.xml