If you need to passsuAfter the command to switch the user, activate the Conda environment, you can follow the following steps:
1. Use su to switch to the target user and activate the environment
In the terminal, use it directlysuSwitch to the target user (normal user), and activate the Conda environment:
su - username
What this command does:
- Switch to
usernameUser. - use
-Ensure the environment of the target user (including.bashrcor.bash_profile）。
Next activate the Conda environment:
conda activate <environment_name>
If Conda is not added toPATHEnvironment variables, please load the Conda environment first:
source /home/username/miniconda3/etc// conda activate <environment_name>
2. Switch users in one step and activate the environment
CansuMerge the Conda activation command into one command:
su - username -c "source /home/username/miniconda3/etc// && conda activate <environment_name> && bash"
explain:
-
su - username: Switch to the target user. -
-c "...": Execute subsequent commands. -
source ...: Load the Conda environment script. -
conda activate ...: Activate the specified Conda environment. -
&& bash: Enter the user's shell (environment with activation).
3. Keep the current Shell activated Conda environment
If you just want to temporarily switch users and activate the Conda environment, you can run the following command without entering the interactive shell:
su - username -c "source /home/username/miniconda3/etc// && conda activate <environment_name> && python --version"
This approach is suitable for performing specific tasks, such as running Python scripts or executing commands in an environment.
4. Configure su, automatically load Conda after switching
Configure the automatic loading of the Conda environment for the target user, in the target user’s~/.bashrcor~/.bash_profileAdded to the file:
Error: su: invalid option – ‘n’ The reason is that the command is not quoted
Error su: Invalid option – ‘n’ occurs because the su command interprets the -n parameter (from the conda run command) as its own option, not the option of the command you are trying to execute.
To resolve this, you need to make sure that the command passed to su is referenced correctly so that it is treated as a single parameter.
Here is the revised command:
su - nginx -c "/home/nginx/miniconda3/bin/conda run -n crisprcasfinder perl -in /data/website_data/data_assets/genomics_begoniaceae/private/crispr/job/CRISPRCasFinder_tzyzd2L0/ -out CRISPRCasFinder_tzyzd2L0 -noMism"
illustrate:
su - nginx: Switch to nginx user and load its environment.
-c: Execute a single command after switching users.
Complete commands in quotes: Make sure everything after -c is treated as a separate string and passed it to the shell as a single command.
Additional Notes:
Ensure Conda's PATH or full path:
If conda is not in the PATH of nginx user, make sure to provide the full path to conda, as shown in the revised command.
Permission Check:
Ensure that nginx users have the correct permissions to execute Perl scripts and access required files and directories.
Activate the environment (optional): If the conda run command does not work as expected, you may need to explicitly activate the environment before running the script. You can adjust the commands as follows:
su - nginx -c "source /home/nginx/miniconda3/etc// && conda activate crisprcasfinder && perl -in /data/website_data/data_assets/genomics_begoniaceae/private/crispr/job/CRISPRCasFinder_tzyzd2L0/ -out CRISPRCasFinder_tzyzd2L0 -noMism"
This ensures that the crisprcasfinder environment is activated correctly before the Perl script is executed.
This article about the su command in dockerfile to switch the user activation environment, and the error su: invalid option -- 'n' is introduced here. For more related dockerfile su command content, please search for my previous article or continue browsing the related articles below. I hope everyone will support me in the future!