Zika-tutorial, NO /snp/bin/docker

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Hi, there:

Please see the error message below. I don’t know why it compalins there is no /snp/bin/docker. I used conda to install nextstrain, not docker.

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Thank you & best regards,
Jie

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@jiehuang001 in this case you may need to run nextstrain build --native --cpus 1 zika-tutorial/. The nextstrain-cli supports a number of runners (docker being one of them), and in your case we wish to use the “native” environment.

You may also find the output printed by nextstrain check-setup helpful. You’ll need at least snakemake & augur to be installed to run the zika-tutorial build (auspice doesn’t need to be installed if you wish to use auspice.us to visualise the output).

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Dear James:

Thank you very much!

I was simply following the nextstrain online documentation step-by-step exactly.
If somehow I need to add “–native” into the following command, can you please add this into the online documentation? Otherwise, many other learners would run into the same issue.

Also, for the next command “nextstrain view zika-tutorial/auspice/” listed in the tutorial, it seems that i need to add “–native” too. Please confirm that this is the case. Please see the screenshot below.

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After I added “–native”, the command runs without error message. But I still could not view anything at http://127.0.0.1:4000/zika. Can you please let me know if I missed something else?

Thank you very much for giving us a wonderful nextstrain!

Best regards,
jie

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I’m not sure why you cannot view anything at that URL – from the screenshot it looks as if it should work. @trs may know more here. In the meantime, you can drag & drop the zika-tutorial/auspice/zika.json file onto https://auspice.us to visualise it.

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@jiehuang001 It looks like you may be running nextstrain view within WSL? I wonder if there’s a port mapping/forwarding issue there. I don’t have much first-hand experience with WSL, so I’m not sure if the network stack is shared between WSL and the Windows host.

As a quick check, can you try running nextstrain view with the --allow-remote-access option and see if the hopefully new URL it suggests works better?