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Using BioGrids

This assumes that you already have BioGrids installed on your system - otherwise, please see the Installing BioGrids Software section with detailed installation instructions.

Step 1: Check If BioGrids Is Already Installed

The BioGrids software collection is accessible from the /programs/ path and is run from the command line in a terminal. To initialize the BioGrids shell environment:

Open a terminal window:

  • macOS: Open Terminal.app (Applications → Utilities → Terminal)
  • Linux: Open your default terminal application

New to using the terminal? See our basic command line resources.

Run ls /programs/biogrids*shrc

  • If this returns /programs/biogrids.cshrc /programs/biogrids.shrc , BioGrids is installed.
  • If this returns something else, such as "No such file or directory" or "no matches found", BioGrids has not been installed correctly; please see Installing BioGrids Software.

Step 2: Check if BioGrids Is Already Available (initialized)

On the terminal window, run: sbinfo

If you see information about BioGrids, your environment is already set up.

If you see "command not found", continue to the next steps.

Step 3: One-Time BioGrids Initialization (Temporary)

  1. Check which shell you are using by typing echo $SHELL and pressing enter (your shell is the program that interprets commands in the terminal). You will see output similar to one of the following:
  2. /bin/bash → bash shell
  3. /bin/zsh → zsh shell

  4. /bin/tcsh or /bin/csh → (t)csh shell

  5. Source the appropriate BioGrids configuration file for your shell:

For bash/zsh: 

source /programs/biogrids.shrc

For (t)csh: 

source /programs/biogrids.cshrc

This command will initialize BioGrids. On initialization, you should see the BioGrids welcome message. If not (if there is a source: no such file or directory error message or similar), BioGrids is not installed. Go to the Installing BioGrids Software section to learn how to install BioGrids.

If you only want to use BioGrids for the current terminal session, run:

source /programs/biogrids.shrc

This enables BioGrids until you close the terminal. You will need to repeat it every time you open a new terminal for using BioGrids.

Setting an alias

If you would prefer to load the BioGrids environment on demand and not have to type the command above, you can set an alias to a shorter command of your choosing.

For example, for bash in ~/.bashrc :

alias bg='source /programs/biogrids.shrc'

For tcsh in ~/.tcshrc, this would be

alias bg 'source /programs/biogrids.cshrc'

To make BioGrids available every time you open a terminal, you must add one line to your shell's startup file.

If You Are Using bash

Edit the file ~/.bashrc:

On a terminal window, run: nano ~/.bashrc

Add this line at the end of the file: source /programs/biogrids.shrc

Save and exit nano: - Press CTRL + O → Enter (save) - Press CTRL + X (exit)

To apply the change, run: source ~/.bashrc (you only have to run this after making a change, not for every new terminal session you start)

If You Are Using zsh (Default on newer macOS)

Edit the file ~/.zshrc: nano ~/.zshrc

Add this line: source /programs/biogrids.shrc

Save and exit: - CTRL + O → Enter - CTRL + X

Apply changes: source ~/.zshrc (you only have to run this after making a change, not for every new terminal session you start)

If You Are Using (t)csh

Edit ~/.cshrc or ~/.tcshrc: nano ~/.cshrc

Add: source /programs/biogrids.cshrc

Save and exit: - CTRL + O → Enter - CTRL + X

Apply changes: source ~/.cshrc (you only have to run this after making a change, not for every new terminal session you start)

Step 5: Verify the Setup

On a terminal window, run (remember to initialize BioGrids before if you have not configured the automatic initialization): sbinfo

You should now see BioGrids information confirming that the environment is active.

Step 6: Using Software Titles Installed with BioGrids

After installation, existing titles in BioGrids can be launched as you have done before outside BioGrids, with no additional configuration!

See how to add, update, and remove titles, and manage your installation here.

Step 7: Change Software Versions

In BioGrids, you can have different versions of any title installed and ready to be used. Check how to manage different software versions installed through BioGrids.

Common Problems & Troubleshooting

Check your installation status

Check your CLI version: biogrids-cli -V

Check BioGrids' latest version here.

Check for manual updates of your installed titles: biogrids-cli updates

Try running sbinfo:

sbinfo: command not found means:

  • BioGrids is not initialized
  • Re-run the source /programs/biogrids.shrc command
  • Confirm you edited the correct startup file for your shell

Changes to .bashrc (or equivalent) didn't take effect:

  • Make sure you initialized (sourced) the startup file after editing
  • Try opening a new terminal window

/programs/biogrids.shrc: No such file or directory:

Need help?

If you run into issues or are unsure about any step: