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Question: How to put uploaded reference file into the Galaxy`s workflow in a pipeline?
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gravatar for msprindzhuk
20 months ago by
msprindzhuk • 50
msprindzhuk • 50 wrote:

How to put uploaded reference file into the Galaxy`s workflow in a pipeline? Is there any tutorial?
workflow upload cloud pipeline • 519 views
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modified 20 months ago by Jennifer Hillman Jackson ♦ 25k • written 20 months ago by msprindzhuk • 50
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gravatar for Jennifer Hillman Jackson
20 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I am not sure exactly what you mean, but if what you want to be able to do is have your custom reference genome available to tools within a workflow (to select as a target "database"), then do the following:

  1. Clean-up the custom reference genome fasta file with the tool NormalizeFasta using the option to wrap at 80 bases and to trim the title line at the first whitespace.
  2. From within the history that contains that custom genome fasta file, go to User > Custom Builds.
  3. Create a short, one word (no spaces) name to the build.
  4. The same value can be used for the description.
  5. Select the cleaned-up custom genome.
  6. Submit. Allow this to process.

Your custom build will now appear in the list of cached genomes and can be used with tools (as a "database" assignment) and within workflows.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 20 months ago by Jennifer Hillman Jackson ♦ 25k
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