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AstrobioMike / GToTree

A user-friendly workflow for phylogenomics
GNU General Public License v3.0
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Install errors with fish shell. #7

Closed vinisalazar closed 5 years ago

vinisalazar commented 5 years ago

Dear @AstrobioMike,

I was installing your program and bumped into a couple of (easy to fix) errors. Nevertheless, I thought you would appreciate me reporting them.

The reason I got this is because I'm using fish shell. So maybe putting a heads-up for your users to use 'normal' bash might prevent them from running into the same errors.

  1. When I run . ./conda-setup.sh I got this error:
./conda-setup.sh (line 32): Unsupported use of '||'. In fish, please use 'COMMAND; or COMMAND'.
source activate gtotree 2> /dev/null || conda activate gtotree
                                      ^
from sourcing file ./conda-setup.sh
    called on line 230 of file /usr/local/Cellar/fish/2.7.1/share/fish/config.fish

in function '.'
    called on standard input

source: Error while reading file './conda-setup.sh'

This was fixed simply by running bash conda-setup.sh, even if I was still using fish.

  1. After installation, fish doesn't recognize the gtt-hmms command. After exiting fish, the command ran smoothly on bash.

Best,

V

AstrobioMike commented 5 years ago

Hi there, Vini,

Thanks so much for sending this in. I of course am trying to make things as portable as possible across all types of unix variants, but do not have the expertise to sufficiently do so, ha. I added a specific note about the fish shell at the top of the install page on the wiki.

Thanks again for taking the time to post this! It's appreciated :) -mike