Question: Is it possible to upload SnpEff databases to Galaxy?
1
gravatar for vladimir.gritsenko
2.1 years ago by
Tel Aviv University
vladimir.gritsenko90 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!

ADD COMMENTlink modified 2.1 years ago by Jennifer Hillman Jackson25k • written 2.1 years ago by vladimir.gritsenko90
1
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink modified 2.1 years ago • written 2.1 years ago by Jennifer Hillman Jackson25k
1

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

ADD REPLYlink written 2.1 years ago by vladimir.gritsenko90

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 REPLYlink written 2.1 years ago by Jennifer Hillman Jackson25k
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