Conda command working in command prompt but not in bash script

Question

my anaconda (4.5.4) works fine as long as I just use it via a linux terminal (bash shell). However, running conda commands in a bash script does not work at all.

The script test.sh containes these lines:

#!/bin/bash
conda --version
conda activate env

Now, running bash test.sh results in the error test.sh: line 2: conda: command not found test.sh: line 3: conda: command not found

As recommended for anaconda version > 4.4 my .bashrc does not contain

export PATH="/opt/anaconda/bin:$PATH",

but

. /opt/anaconda/etc/profile.d/conda.sh

Thank you.

Answer 1

I solved the problem thanks to @darthbith 's comment.

Since conda is a bash function and bash functions can not be propagated to independent shells (e.g. opened by executing a bash script), one has to add the line

source /opt/anaconda/etc/profile.d/conda.sh

to the bash script before calling conda commands. Otherwise bash will not know about conda.

Answer 2

If @randomwalker's method doesn't work for you, which it won't any time your script is run in a more basic shell such as sh, then you have two options.

1. Add this to your script: eval $(conda shell.bash hook)

2. Call your script with: bash -i <scriptname> so that it runs in your interactive environment.