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package.json: run shell scripts with env bash #868

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merged 1 commit into from
Feb 10, 2020

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Artoria2e5
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@Artoria2e5 Artoria2e5 commented Jan 30, 2020

This should be all it takes to keep node from trying to run them with cmd on Windows. Closes #867.

(And yes, it installs in git bash -- the bash that comes with git for windows -- now.)

This should be all it takes to keep node from trying to run them with cmd on Windows. Closes nextstrain#867.
@Artoria2e5 Artoria2e5 requested a review from trvrb February 8, 2020 03:41
@trvrb trvrb requested a review from tsibley February 10, 2020 02:30
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trvrb commented Feb 10, 2020

Thanks so much for the PR @Artoria2e5! Much appreciated. @tsibley: Could you review this? You're better at this sort of cross-platform thing than I am.

@trvrb trvrb removed their request for review February 10, 2020 02:32
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This looks good to me and works on Linux. I can't quickly test on Windows right now, but I trust it works there.

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Tested on MacOS and everything still works 👍

@jameshadfield jameshadfield merged commit 68df5ce into nextstrain:master Feb 10, 2020
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babarlelephant commented Feb 5, 2021

Auspice worked on windows 7 32bit with node 8, after adding cygwin/bin to the path ie. set PATH=%PATH%;c:\code\cygwin\bin(for calling env bash), it fails with node 6 at puppeteer/puppeteer#5428

@jameshadfield
A similar problem in augur : I needed to replace augur align by python ../augur-master/bin/augur align in zika_tutorial/Sakemake and
cmd = "mafft
by
cmd = "env bash /cygdrive/c/code/cygwin/usr/local/bin/mafft
in augur-master\augur\align.py
This way augur calls the mafft in cygwin and it works fine, I got zika.json which worked in auspice.

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Make it work on Windows
5 participants