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Reference Genomes in Galaxy

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Authors: orcid logoDaniel Blankenberg avatar Daniel Blankenbergorcid logoSimon Gladman avatar Simon Gladman
Published: Jan 28, 2019
Last Updated: Apr 18, 2023

Overview

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Built in Data

List_of_data.png

Data, what data?

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Overview

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Data schematics in Galaxy

schematic

Using reference data in a tool

bwa.xml

<conditional name="reference_source">
      <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See 'Indexes' section of help below">
        <option value="cached">Use a built-in genome index</option>
        <option value="history">Use a genome from history and build index</option>
      </param>
      <when value="cached">
        <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
          <options from_data_table="bwa_mem_indexes">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No indexes are available" />
          </options>
          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
        </param>
      </when>
      <when value="history">

Where are the data tables?

tool_data_table_conf.xml

(Usually located in galaxy/config/)

  <tables>
    <!-- Locations of indexes in the BWA mapper format -->
    <table name="bwa_mem_indexes" comment_char="#" allow_duplicate_entries="False">
      <columns>value, dbkey, name, path</columns>
      <file path="tool-data/bwa_index.loc" />
    </table>
  </tables>

“loc” files - Short for location!

bwa_index.loc

#
#<unique_build_id>   <dbkey>   <display_name>   <file_path>
#
bosTau7 bosTau7 Cow (bosTau7)   /genomes/bosTau7/bwa_mem_index/bosTau7/bosTau7.fa
ce10    ce10    C. elegans (ce10)       /genomes/ce10/bwa_mem_index/ce10/ce10.fa
danRer7 danRer7 Zebrafish (danRer7)     /genomes/danRer7/bwa_mem_index/danRer7/danRer7.fa
dm3     dm3     D. melanogaster Apr. 2006 (BDGP R5/dm3) (dm3)   /genomes/dm3/bwa_mem_index/dm3/dm3.fa
hg19    hg19    Human (hg19)    /genomes/hg19/bwa_mem_index/hg19/hg19.fa
hg38    hg38    Human (hg38)    /genomes/hg38/bwa_mem_index/hg38/hg38.fa
mm10    mm10    Mouse (mm10)    /genomes/mm10/bwa_mem_index/mm10/mm10.fa

Overview

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Some Problems!

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Typical conversation

Hi, We have a local install of galaxy andI’m trying to add the reference index files for bwa using the information provided in the following link:

…

I have modified the bwa_index.loc file present in the ../tool-data directory by adding the path to where the index is on our server (Also attached). However, even after restarting the server, the ference genome does not show when choosing the “use a built in index option”. I’m not sure whether the loc file is correctly created, and whether any other configuration file needs to be changed/updated. Help in the matter greatly appreciated

Thanks, Aarti

Typical conversation

Hi Aarti, Check the name of your rf file. If it is hg19.fa, then modified the loc file as “hg19 hg19 HG19_BWA /root/Ref_INDEX/HG19BWAIndex/base/hg19.fa”

Avik Datta

Typical conversation

Also make sure you are using TABs to separate the fields in the .loc file, this has bitten me several times in the past. My vim config places 4 spaces instead of TAB, to deactivate this optin you can do “:set noexpandtab”

Hope it helps, Carlos

Typical conversation

Hello Carlos, Thanks a lot for the tip. The tab trick has fixed the problem.

Regards, Aarti

Other concerns

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Overview

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Data Managers

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Data Managers

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Special class of Galaxy tool

Looks just like a normal Galaxy tool!

Data-manager-ui.png

What does it do?

The output of the data manager is a JSON description of the new data table entry

data_table_JSON.png

This gets turned into a new data table entry

data_table_entry.png

The index files themselves get placed in the appropriate location.

Data Managers Admin

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Data Managers Admin

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Resources / further reading

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https://galaxyproject.org/admin/tools/data-managers/ ]

Exercise Time!

Overview

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There’s a lot of reference data

.large[ (and it’s hard to keep up with) ] ref_data_prob_flow.png

CernVM-FS to the rescue

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CVM-FS Global Structure

.widen_image[ cvmfs_global_structure.png ]

Exercise #2:

.large[ Connect our instances to CVMFS for reference data ]

Thank you!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors! page logo Tutorial Content is licensed under Creative Commons Attribution 4.0 International License.