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Question: Run Megablast on Galaxy against local genome
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gravatar for ingerid.hagen
2.6 years ago by
ingerid.hagen • 0
ingerid.hagen • 0 wrote:

Hey, Does anyone know how I can run Megablast on Galaxy with a reference genome that is not yet online, but available locally on my computer. Many thanks, Ingerid Hagen
galaxy • 640 views
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modified 2.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.6 years ago by ingerid.hagen • 0
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gravatar for Jennifer Hillman Jackson
2.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Setting up a local or cloud Galaxy of your own is how to use Megablast with alternate genomes.

https://wiki.galaxyproject.org/BigPicture/Choices

Obtain the tool from the Tool Shed (http://getgalaxy.org/toolshed) but install the data according to these older rules (scroll down to Megablast section: https://wiki.galaxyproject.org/Admin/DataPreparation). In short, formatdb the genome, adjust the loc and builds files, then restart the server. The test is that if megablast will run line-command with given inputs/parameters/indexes, the server has the resources to run megablast within Galaxy given the same.

Best, Jen, Galaxy team
ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k
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