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Add genomics-workspace workflow #73

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mpoelchau opened this issue Sep 20, 2019 · 1 comment
Closed

Add genomics-workspace workflow #73

mpoelchau opened this issue Sep 20, 2019 · 1 comment
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@mpoelchau
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We want to add a workflow to add a new organism and sequence files to the genomics-workspace app, as part of the organism onboarding workflow.

See also NAL-i5K/genomics-workspace#280

Steps/example commands:

  • addorganism : python manage.py addorganism [genus] [species]
  • addblast : python manage.py addblast [genus] [species] -t [sequence type] -f [path to fasta file]
  • makeblastdb : python manage.py blast_utility [path to fasta file] -m
  • populatesequence : python manage.py blast_utility [path to fasta file] -p
  • addhmmer : python manage.py addhmmer [genus] [species] -f [path to fasta file]
  • make blast is_shown:
    python manage.py blast_shown [path to fasta file] --shown [true/false]
@mpoelchau
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Added in #79, #76, and #74.

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