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:
data.galaxyproject.org
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Description: | The usegalaxy.org CVMFS repository hosts more than 4 TB of reference data. There are two primary directories in the reference data repository:
Currently, the Laniakea instances are preconfigured to mount For GDC Somatic Variant flavour (GDC Somatic Variant on Galaxy) Galaxy is configured to use also an additional |
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elixir-italy.covacs.refdata
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Description: | This repository hosts specific reference data for CoVaCS pipeline, Laniakea configure the CoVaCS flavours to consume these data. |
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Reference data cvmfs | Details |
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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
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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. |
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Reference data cvmfs | Details |
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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 |