How to fix "set -e -o pipefail" (CentOS script) for Ubuntu 18.04 LTS?

Asked Feb 18 '21 at 14:33

Active Feb 18 '21 at 15:29

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I'm working with a set of scripts that automate some bioinformatics (mitoVGP; https://github.com/VGP/vgp-assembly/tree/master/mitoVGP) and then the install is done as a conda environment.

The problem (sh symlinked to dash, as opposed to bash) has been outlined by @SergiyKolodyazhnyy in the first answer here: "set -e -o pipefail" not working on bash script on Ubuntu 16

So, my question is, how do I fix these scripts, or else make it such that invoking them with makes them such that they work/run in a bash environment on Ubuntu?

edited Feb 18 '21 at 15:29

muru

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asked Feb 18 '21 at 14:33

Andor Kiss

OK I am confused are you running Cent-OS 16.04 or 18.04? – David Feb 18 '21 at 14:42
How do you run the scripts? – choroba Feb 18 '21 at 14:45
1

Which particular scripts are you having this issue with? I just looked at every script under vgp-assembly/mitoVGP/scripts/ and they all appear to have the shebang #!/bin/bash – steeldriver Feb 18 '21 at 16:05
Running under 18.04 LTS, not CentOS. Started with <./mitoVGP [options] input_file> – Andor Kiss Feb 18 '21 at 16:37
Yes, I know the shebang states '#!/bin/bash', but the O/S (Ubuntu) doesn't actually run the script in bash, it goes back to dash. This is my original question/problem. – Andor Kiss Feb 18 '21 at 16:52

How to fix "set -e -o pipefail" (CentOS script) for Ubuntu 18.04 LTS?

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