I am hoping to run a simple shell script to ease the management around some conda environments. Activating conda environments via conda activate in a linux os works fine in the shell but is problematic within a shell script. Could someone point me into the right direction as to why this is happening?
Example to repeat the issue:
# default conda env
$ conda info | egrep "conda version|active environment"
active environment : base
conda version : 4.6.9
# activate new env to prove that it works
$ conda activate scratch
$ conda info | egrep "conda version|active environment"
active environment : scratch
conda version : 4.6.9
# revert back to my original conda env
$ conda activate base
$ cat shell_script.sh
#!/bin/bash
conda activate scratch
# run shell script - this will produce an error even though it succeeded above
$ ./shell_script.sh
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
Currently supported shells are:
- bash
- fish
- tcsh
- xonsh
- zsh
- powershell
See 'conda init --help' for more information and options.
IMPORTANT: You may need to close and restart your shell after running 'conda init'.
I use 'source command' to run the shell script, it works:
source shell_script.sh
The error message is rather helpful - it's telling you that conda is not properly set up from within the subshell that your script is running in. To be able to use conda within a script, you will need to (as the error message says) run conda init bash (or whatever your shell is) first. The behaviour of conda and how it's set up depends on your conda version, but the reason for the version 4.4+ behaviour is that conda is dependent on certain environment variables that are normally set up by the conda shell itself. Most importantly, this changelog entry explains why your conda activate and deactivate commands no longer behave as you expect in versions 4.4 and above.
For more discussion of this, see the official conda issue on GitHub.
Edit: Some more research tells me that the conda init function mentioned in the error message is actually a new v4.6.0 feature that allows a quick environment setup so that you can use conda activate instead of the old source activate. However, the reason why this works is that it adds/changes several environment variables of your current shell and also makes changes to your RC file (e.g.: .bashrc), and RC file changes are never picked up in the current shell - only in newly created shells. (Unless of course you source .bashrc again). In fact, conda init --help says as much:
IMPORTANT: After running conda init, most shells will need to be closed and restarted for changes to take effect
However, you've clearly already run conda init, because you are able to use conda activate interactively. In fact, if you open up your .bashrc, you should be able to see a few lines added by conda teaching your shell where to look for conda commands. The problem with your script, though, lies in the fact that the .bashrc is not sourced by the subshell that runs shell scripts (see this answer for more info). This means that even though your non-login interactive shell sees the conda commands, your non-interactive script subshells won't - no matter how many times you call conda init.
This leads to a conjecture (I don't have conda on Linux myself, so I can't test it) that by running your script like so:
bash -i shell_script.sh
you should see conda activate work correctly. Why? -i is a bash flag that tells the shell you're starting to run in interactive mode, which means it will automatically source your .bashrc. This should be enough to enable you to use conda within your script as if you were using it normally.
Quick solution for bash: prepend the following init script into your Bash scripts.
eval "$(command conda 'shell.bash' 'hook' 2> /dev/null)"
Done.
For other shells, check the init conf of your shell, copy the following content within the shell conf and prepend it into your scripts.
# >>> conda initialize >>>
...
# <<< conda initialize <<<
You can also use
conda init --all --dry-run --verbose
to get the init script you need in your scripts.
Explanation
This is related with the introduction of conda init in conda 4.6.
Quote from conda 4.6 release log
Conda 4.4 allowed “conda activate envname”. The problem was that setting up your shell to use this new feature was not always straightforward. Conda 4.6 adds extensive initialization support so that more shells than ever before can use the new “conda activate” command. For more information, read the output from “conda init –help”
After conda init is introduced in conda 4.6, conda only expose command
conda into the PATH but not all the binaries from "base". And environment switch is unified by conda activate env-name and conda deactivate on all platforms.
But to make these new commands work, you have to do an additional initialization with conda init.
The problem is that your script file is run in a sub-shell, and conda is not initialized in this sub-shell.
References
Conda 4.6 Release
Unix shell initialization
Shell startup scripts
Using conda activate or source activate in shell scripts does not always work and can throw errors like this. An easy work around it to place source ~/miniconda3/etc/profile.d/conda.sh above any conda activate command in the script:
source ~/miniconda3/etc/profile.d/conda.sh # Or path to where your conda is
conda activate some-conda-environment
This is the solution that has worked for me and will also work if sharing scripts. This also gets around having to use conda init as on some clusters I have worked with the system is initialised but conda activate still won't work in a shell script.
if you want to use the shell script to run the other python file in the other conda env, just run the other file via the following command.
os.system('conda run -n <env_name> python <path_to_other_script>')
What is the problem with simply doing something like this in your shell:
source /opt/conda/etc/profile.d/conda.sh
(The conda init is still marked as Experimental, and thus not sure if it is a good idea to use it yet).
I also had the exact same error when trying to activate conda env from C++ or Python file. I solved it by bypassing the conda activate statement and using the absolute path of the specific conda env.
For me, I set up an environment called "testenv" using conda.
I searched all python environments using
whereis python | grep 'miniconda'
It returned a list of python environments. Then I ran my_python_file.py using the following command.
~/miniconda3/envs/testenv/bin/python3.8 my_python_file.py
You can do the same thing on windows too but looking up for python and conda python environments is a bit different.
This answer from Github worked for me (I'm using Ubuntu so it's not for Windows only):
eval "$(conda shell.bash hook)"
conda activate my_env
I just followed a similar solution like the one from hong-xu
So to run a shell command that calls the script with arguments and using a specific conda environment:
from a jupyter cell, goes like this :
p1 = <some-value>
run = f"conda run -n {<env-name>} python {<script-name>.py} \
--parameter_1={p1}"
!{run}
I didn't find any of the above scripts useful. These are fine if you want to run conda in non-interactive mode, but I'd like to run it in interactive mode. If I run:
conda activate my_environment
in a bash script it just runs in the script.
I found that creating an alias in .bashrc is all that is required to change directory to a particular project I'm working on, and set up the correct conda environment for me. So I included in .bashrc:
alias my_environment="cd ~/subdirectory/my_project && conda activate my_environment"
and then:
source ~/.bashrc
Then I can just type at the command line:
my_environment
to change to the correct project and correct environment everytime I want to work on a different project.
This answer is similar to #Lamma answer. This worked for me ->
(1) I defined several variables; the conda activate function, environments directory and environment
conda_activate=~/anaconda3/bin/activate
conda_envs_dir=~/anaconda3/envs
conda_env=<env name>
(2) I source conda activate with the environment
source ${conda_activate} ${conda_envs_dir}/${conda_env}
(3) then you can run your python script
python <path to script.py>
This bypasses the conda init requirement. my .bashrc already was initialized and sourcing the .bashrc file didn't work for me. #Lamma's answer worked for me as well as the above code.
The problem is that when you run the bash script, a new (linux) shell environment is created that was not initialized properly. If your intention is to activate a conda environment, and then run python through the script, you can properly initialize the created shell
environment as discussed in the accepted solution.
If however you want to have the conda environment active after you finish this script, then this will not work because the conda environment has changed on the new shell and you exit that shell when you finish the script. Think of this as running bash, then conda activate... then running exit to exit that bash... More details in How to execute script in the current shell on Linux?:
TL;DR:
Add the line #!/bin/bash as the first line of the script
Type the command source shell_script.sh or . shell_script.sh
Note: . in bash is equivalent to source in bash.
$ conda activate scratch
or
$ source activate scratch
#open terminal or CMD as administrator
$ cd <path Anaconda3 install>\Scripts
$ activate
$ cd ..
$ conda activate scratch
I am running some bash scripts that submit sbatch scripts after doing some stuff and I want to check if the conda environment requierd for the tools in the sbatch script to work exists and then that this named conda environment matches the contents of a conda environment yml file.
So essentially this:
test ! -d ~/miniconda3/envs/fungal-hybrid-assembly || echo "Conda environment does not exist. Initialising conda environment......" && conda create fungal-hybrid-assembly.yml
But testing that the fungal-hybrid-assembly environment actually contains the correct packages rather than it just existing.
I want to run this code:
#! /bin/sh
env_name="base"
source activate $env_name
in my shell as sh filename.sh, but an error say:
filename.sh: source: not found
with the following line:
filename.sh: Syntax error: Unterminated quoted string
what is the problem? It is good to say that I can run this command in shell manually but when I try to run as shell script this problem gives me the error. any help appreciated.
There is no command named source in POSIX shell. To source a file, use a period, i.e.
. filename.sh
Options
You have three options:
Login Mode - use a shell in login mode that automatically sets up Conda's shell functionality.
Manual initialization - where you manually source the shell-appropriate initialization script to enable conda activate functionality in your script.
conda run - where you let Conda auto-activate the env for you.
1: Login Mode
Typical Conda installations have users run conda init for their primary shell, which adds code to the user's shell-specific resource file (e.g., .bashrc). The current way OP runs the script, and the script's shebang, will never load such a resource and therefore do not define the conda activate function.
Instead, redefine the shebang to use a full shell and run in login mode. For example, this would be the BASH version:
#!/usr/bin/env bash -l
and run with either
. filename.sh
or
bash -l filename.sh
This assumes the user has run conda init bash.
2: Manual Initialization
The conda activate functionality is normally a shell function that Conda creates at the start up of your interactive shells. To use this same functionality in scripts, you can manually run the initialization script. Assuming a bash type shell, this is located under the base Anaconda/Miniconda directory at etc/profile.d/conda.sh. Let's assume you have it at:
/Users/user/miniconda3/etc/profile.d/conda.sh
A working version of your script would then go something like
#!/bin/sh
. /Users/user/miniconda3/etc/profile.d/conda.sh
conda activate base
...
3: Conda Run
You can use conda run (see conda run --help) in the shebang to automatically activate the env and run everything in the script in that context. This assumes that you have properly configured your shell to use conda. For example,
#!/usr/bin/env conda run -n base bash
some_cmd
where some_cmd is a commandline program that is available in your env.
I have a conda environment that I created with a path (conda create -p /full/path/to/env). When I activate the environment it displays the full path to the environment in parentheses at the beginning of the command prompt line. like
(full/path/to/env) [username#server]
I want to change it so it just shows env instead of full/path/to/env. How do I do that?
I tried adding the directory leading up to my conda environment (i.e. full/path/to) to my env_dirs configuration using conda config but that didn't work.
I want to dynamically store in the project directory, how can I do that?
I have searching and found this Can I choose where my conda environment is stored? but this not dynamically store my conda environment to the project directory like virtualenv do
Use --prefix, -p for conda create instead of --name, -n.
$ conda create --help
...
Target Environment Specification:
-n ENVIRONMENT, --name ENVIRONMENT
Name of environment.
-p PATH, --prefix PATH
Full path to environment location (i.e. prefix).
...
Usage
conda create -p ./venv python=3.6
conda env list
# activate the local environment with relative or absolute path
conda activate ./venv
conda deactivate
# remove the env
conda env remove -p ./venv
# or just delete the "venv" folder directly
Note: When you set a specific path for your environment with -p, -n is not allowed, which means you cannot give the env a name in this case. You have to operate this kind of envs with their paths.