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Test and update documentation around comma-separated list for taxa #35

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kbshimmyo opened this issue Mar 9, 2018 · 1 comment
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@kbshimmyo
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The released version of the genome downloader should support comma-separated lists. "This is supported in the 0.2.6 release that I just pushed to github and pypi." (Response to Issue 55 on their github).

  1. We should test our wrapper script with comma-separated list - at least these two cases:
    "correct" formulation: something1, something2, something3
    trailing delimiter: something1, something2, something3,

(If the trailing delimiter breaks things, we should document that for the user because it's easy to end up with that from quick-and-dirty concatenation scripts.)

  1. Assuming that works, we should update (not remove) the first caveat in the documentTaxList function of the wrapper script. We should not remove the information because users may be using a previously installed version of genome downloader. Could change

echo " The released ncbi-genome-downloader currently does not accept a comma-separated list."
to
echo " Versions of the ncbi-genome-downloader earlier than 0.2.6 do not accept a comma-separated list. Upgrade to the latest version for this functionality."

@gedankenstuecke
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Hey, I just gave it a spin on my end and using a comma-separated list works if you're running the 0.2.6 version of the NCBI genome downloader. Having said this: To get the version 0.2.6 I still had to clone their repository and do pip install . from that clone, PyPI did continue to give me the older version. But either way I think we can update the caveat as upcoming versions will support this.

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