Assign dbkey to already downloaded ncbi databases

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Question: Assign dbkey to already downloaded ncbi databases

7 days ago by

feliyon • 10

Peru/Lima

feliyon • 10 wrote:

Hello Community,

I have a question about how to assign the dbkey for already downloaded NCBI databases, like other genomics or refseq_genomic. Since for adding single genome with their dbkey I have used the data manager fetch... but this for single cases. We have already downloaded several nucleotide NCBI databases but we will like to add them all to appear as indexed within Galaxy, what will be the right procedure?

Thanks in advance, Felipe

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modified 1 day ago by Jennifer Hillman Jackson ♦ 25k • written 7 days ago by feliyon • 10

1 day ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Each genome will need to be fetched and then indexed for the tools that require additional indexes. It is generally a good idea to index all genomes for samtools, picard, and 2bit. Then index for other tools as wanted.

The fetch DM can use fasta inputs from the history or it can retrieve data from selected sources. A dbkey with .len data is created either way.

This can be done with Data Managers individually, or you can use the utility Ephemeris to process the data in batch. You'll need to have the target DMs installed on your server before using it.

Thanks! Jen, Galaxy team

ADD COMMENT • link written 1 day ago by Jennifer Hillman Jackson ♦ 25k

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