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make shell scripts conform to shellcheck standards #962

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joachimschmidt557
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This basically just includes missing shebangs, some quoting and removing reference to a variable never assigned to.

@jameshadfield jameshadfield temporarily deployed to auspice-scripts-shellch-ay9jzl March 22, 2020 22:46 Inactive
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jameshadfield commented Mar 22, 2020

@tsibley could you check these shebangs are ok with you? (I normally use usr/bin/env bash but that may have its own problems). thanks

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tsibley commented Mar 23, 2020

@jameshadfield /bin/bash is basically universal and what I use for Bash shebangs. I'd stick with it.

I would expect /usr/bin/env bash to also work nearly all the time, but the use cases for allowing PATH to determine which bash to run seem vanishingly small and in terms of hardcoding paths it just swaps one for another.

@jameshadfield jameshadfield merged commit 8ab32f7 into nextstrain:master Mar 23, 2020
@joachimschmidt557 joachimschmidt557 deleted the scripts-shellcheck branch March 23, 2020 08:47
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3 participants