Bedtools / FisherBed reference genome

Question: Bedtools / FisherBed reference genome

5 weeks ago by

o.mikh90 • 10 wrote:

Hi, I was trying to run the FisherBed tool from the BedTools on the main galaxy server usergalaxy.org), and the only two reference genomes that appear on the list of locally installed genome files are the hg19 and the brown kiwi genome :) Could you please add the mouse (mm10) and Drosophila (dm6) genomes into the library? I'm afraid that if I upload the genome file from my history it may eat up most of the space..

Many thanks, Olga

reference genome mm10 galaxy bedtools fisherbed • 114 views

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modified 5 weeks ago by Jennifer Hillman Jackson ♦ 25k • written 5 weeks ago by o.mikh90 • 10

5 weeks ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Olga,

The tool is accessing an incorrect reference data table to retrieve the indexes (and is why there are only those two -- both involved special handling/data tables).

I'll need to report this to the developers to get it corrected at the source, update the tool, update the servers, etc. This will take some time. Galaxy EU https://usegalaxy.eu/ also has a limited number of genomes (and not the ones you wish to use). Galaxy Australia https://usegalaxy.org.au/ has the same content as Galaxy Main, so is not an alternative either. The correction will need to be applied to all.

Please use the custom genomes from the history for now. If you need more quota space to accommodate them, please send an email from your registered account email address to galaxy-bugs@lists.galaxyproject.org that includes a link to the post and we can grant you a bit more.

FAQ: Preparing and using a Custom Reference Genome or Build https://galaxyproject.org/learn/custom-genomes/

Thanks for reporting this -- it hadn't been noticed earlier for this tool suite but I recognize the root problem from a prior, similar tool correction that also involved adjusting the index table referenced by the tool wrapper itself.

Best, Jen, Galaxy team

ADD COMMENT • link modified 5 weeks ago • written 5 weeks ago by Jennifer Hillman Jackson ♦ 25k

It looks like this was a problem before, perhaps fixed at some point (not confirmed), and is a problem again (or still). This is the ticket. I asked for a re-review and correction, please follow if interested: https://github.com/galaxyproject/tools-iuc/issues/720

ADD REPLY • link written 5 weeks ago by Jennifer Hillman Jackson ♦ 25k

Many thanks Jen, I appreciate! Best, Olga

ADD REPLY • link written 5 weeks ago by o.mikh90 • 10

Update: The genomes are now available at Galaxy Main https://usegalaxy.org.

Galaxy EU https://usegalaxy.eu and Galaxy AU https://usegalaxy.org.au will be updated next, see the same issue ticket for details.

ADD REPLY • link written 4 weeks ago by Jennifer Hillman Jackson ♦ 25k

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