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Question: Is it possible to upload SnpEff databases to Galaxy?
1
gravatar for vladimir.gritsenko
2.4 years ago by
vladimir.gritsenko • 90
Tel Aviv University
vladimir.gritsenko • 90 wrote:

I have created a database with SnpEff 4.0, which should be compatible with Galaxy. Is it possible to upload this database to Galaxy for use with SnpEff? If yes, how?

EDIT: as a corollary, it seems relatively easy to add a database-installing tool, though I haven't found it.

Thanks!
snpeff toolshed data-managers variant-annotation • 1.0k views
ADD COMMENT • link •
modified 2.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.4 years ago by vladimir.gritsenko • 90
1
gravatar for Jennifer Hillman Jackson
2.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The data cannot be uploaded and used at Galaxy Main (http://usegalaxy.org), but it can be used in a local or cloud Galaxy. The SnpEff Data Manager can be used (repository: data_manager_snpeff - it contains two tools). Be sure to prepare the base genome with the DMs for fasta loading, samtools, and picard first, also available in the Tool Shed, then run this one.

Best, Jen, Galaxy team
ADD COMMENT • link modified 2.4 years ago • written 2.4 years ago by Jennifer Hillman Jackson ♦ 25k
1

Thank you for the reply! It's a pity this functionality is missing. Can you consider adding it?

ADD REPLY • link written 2.4 years ago by vladimir.gritsenko • 90

The genomes supported at http://usegalaxy.org for this tool are currently fixed (as far as I know). However, if you wish to make a request for a built-in index for review, post at this Github ticket: https://github.com/galaxyproject/galaxy/issues/1470

ADD REPLY • link written 2.4 years ago by Jennifer Hillman Jackson ♦ 25k
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