Question: Convert Kraken data to Galaxy taxonomy - missing database (usegalaxy)?
1
gravatar for vebaev
22 months ago by
vebaev130
vebaev130 wrote:

Hi, I'm trying to use Convert Kraken data to Galaxy taxonomy representation (Galaxy Version 1.1), but on the field "Select a taxonomy database" there is nothing to select? Is this should be something from my history or?

kraken • 1.0k views
ADD COMMENTlink modified 22 months ago by Jennifer Hillman Jackson25k • written 22 months ago by vebaev130

I can reproduce this at http://usegalaxy.org. The Kraken tool is undergoing some dependency updates and this particular reference data is missing right now (it consists of pre-computed indexes, not data from the history). More feedback soon - possibly with a ticket to create/add in the reference data. Thanks for reporting the problem. Jen, Galaxy team

ADD REPLYlink written 22 months ago by Jennifer Hillman Jackson25k

I want also to make this database on my local Galaxy can you advice how to do that? I have installed NCBI taxonomy downloader (Galaxy Version 1.0.0), but it asks for "Enter URL for taxonomy files" and I do not know what to enter?

Is it this way to build such database for Convert Kraken data to Galaxy taxonomy for Krona chart use (for Bacterial 16s metagenomics)? Or I'm in the wrong track?

ADD REPLYlink modified 22 months ago • written 22 months ago by vebaev130

I haven't done this myself yet within Galaxy, but others from our team have. I will look into it while doing other the tests/reviews and include the how-to in my reply later.

ADD REPLYlink written 22 months ago by Jennifer Hillman Jackson25k

Related post (for data) https://biostar.usegalaxy.org/p/21309

ADD REPLYlink written 22 months ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
22 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This is the ticket to restore the Kraken indexes for this tool at http://usegalaxy.org: https://github.com/galaxyproject/galaxy/issues/1679

The taxonomy files can be found at NCBI - here is a description (you most likely want the complete nucleotide file): ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid.readme

Best, Jen, Galaxy team

ADD COMMENTlink written 22 months ago by Jennifer Hillman Jackson25k
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