Im trying to extract current working directory and activate conda environment using bash script. My shell script
app_path=$(dirname $(readlink -f $0))
source /conda/bin/activate $app_path;
This issue im facing is when I run the script as
sh script.sh
it is not activating the conda env
If i run with source script.sh
It is not able to recognise readlink command. How to get both of them working together?
Related
I am trying to create a Bash script that downloads a .sh file, runs it to install a program (Anaconda for Python), then run the command conda init to activate the default Anaconda environment base
However, running my bash script as shown
# !#/bin/bash
wget https://repo.anaconda.com/archive/Anaconda3-2021.05-Linux-x86_64.sh
bash Anaconda3-*-Linux-x86_64.sh -b
echo 'export PATH=~/anaconda3/bin:$PATH' >> ~/.bashrc
source ~/.bashrc
conda init
conda env create -f environment.yml
gives the error
./foo.sh: line 6: conda: command not found
./foo.sh: line 7: conda: command not found
Why is conda not found when trying to use it from within the Bash script, but is found if I relogin to the terminal?
How can we fix the Bash script so that using conda works?
I want to use snakemake with fish shell and conda environments in my managed environment (basically I have no root rights and the default shell cannot be changed).
I set up fish as the 'default' shell using this hack inside the .bashrc:
if [ "$REALBASH" != "1" ]; then
case "$-" in
*i*)
export SHELL=/usr/bin/fish
tty > /dev/null && echo "Your ~/.bashrc is switching interactive SHELL to $SHELL"
[ -x $SHELL ] && exec $SHELL "$#"
echo "Apparently $SHELL is not available here. Continuing with bash."
export SHELL=/bin/bash
;;
esac
fi
There is also a command realbash that sets the environment variable REALBASH=1 to bypass this hack.
I managed to get conda to work with fish using this, but it has the disadvantage that within fish the command to activate conda environments is different from bash. In bash, the command is source activate ... and in fish it is conda activate ....
Activating environments works both from bash using source activate ... and from fish using conda activate ....
When I now execute snakemake from fish, I get the following error:
Activating conda environment ...
source: Error encountered while sourcing file “activate”:
source: No such file or directory
If I execute snakemake from bash, the same error occurs.
If I execute snakemake from bash via snakemake --overwrite-shellcmd realbash, I get the same error and end up in the bash shell that was opened by snakemake. Only after typing exit, snakemake completes (but unsuccessfully, of course).
If I execute snakemake from fish via snakemake --overwrite-shellcmd realbash, the same behaviour occurs.
I am confused by the behaviour of --overwrite-shellcmd, is there a way to make this work with my hack?
Otherwise, can I configure snakemake to call conda activate instead of source activate?
Or is there any other solution to this?
Apparently this was a bug in an older version of snakemake. The effects described in the question were produced with snakemake 4.3.1.
Running snakemake from within a conda environment where snakemake 5.17.0 is installed works perfectly fine with the setup as described in the question. No --overwrite-shellcmd or other changes are required.
I am trying to run a command after setting up an environment. This command runs a python script which depends on the environment.
I have the following code:
#!/bin/bash
source ~/some/linux/env/shell
python test.py
However, the "python test.py" only runs after I exit the env shell.
I want to be able to run the "python test.py" inside this new shell env.
Firstly adding python running and interpreting directory.
#!/usr/bin/env python
And you have to give a code execution authority. You can give a permission below
chmod a+x test.py
Now you can run it from the command line.
./test.py
I want to set env variable in shell script. Shell script content is:
#!/bin/bash
export XDEBUG_CONFIG="idekey=PHPSTORM"
I tried both bash bin/enable_debug and bin/enable_debug. After both command I get:
$ echo $XDEBUG_CONFIG
$
However if I run export XDEBUG_CONFIG="idekey=PHPSTORM" directly in cli it works. What's wrong with my method?
You can try running your script as below:
. bin/enable_debug
OR
source bin/enable_debug
as indicated by #Aserre
I'm trying to activate my pyenv-virtualenv environment through very simple bash script like this.
set -e
pyenv activate myenv
But I can't activate my env with below error:
Failed to activate virtualenv.
Perhaps pyenv-virtualenv has not been loaded into your shell properly.
Please restart current shell and try again.
I can activate it in command line, so I think it's due to my shell environment.
I use fish shell, but it's launched after $PATH settings read in bash shell.
I show you my settings.
.bash_profile:
export LANG="ja_JP.UTF-8"
export XDG_CONFIG_HOME="$HOME/.config"
export PATH="/sbin"
export PATH="/usr/sbin:$PATH"
export PATH="/bin:$PATH"
export PATH="/usr/bin:$PATH"
export PATH="/usr/local/bin:$PATH"
export PYENV_ROOT="$HOME/.pyenv"
export PATH="$PYENV_ROOT/bin:$PATH"
exec fish
And my config.fish:
status --is-interactive; and source (pyenv init -|psub)
status --is-interactive; and source (pyenv virtualenv-init -|psub)
What's wrong?
I'm using:
OS: OS X 10.13.5
fish: v2.7.1
pyenv: v1.2.5
pyenv-virtualenv: v1.1.3
I believe the cause is that you are initializing PyEnv in the Fish shell environment but then calling PyEnv in the Bash shell environment (via your Bash script). To solve this problem, you could try either of the following potential solutions:
Initialize PyEnv in your Bash environment (in addition to your Fish environment)
Write your script in Fish instead of Bash
Since PyEnv seems so have better support for Bash than Fish, let's focus on option #1. Step 3 of the PyEnv installation guide suggests the following command for adding PyEnv initialization to your ~/.bash_profile:
$ echo -e 'if command -v pyenv 1>/dev/null 2>&1; then\n eval "$(pyenv init -)"\nfi' >> ~/.bash_profile
After running that command, I suspect your script will function as you expect. If it does not, you could try adding the same PyEnv initialization snippet (that you just added to your ~/.bash_profile) to the top of your Bash script.