Convenience Scripts

It’s common that you’ll find yourself using a particular script again and again in various contexts. If such is the case, it would be useful to be able to call those scripts repeatedly from your PATH instead of specifying (and remembering) their location each time. To do that, you just need to create a folder and make sure it’s exported in your PATH.

Creating a script folder

Create the folder

The location of this folder is usually most convenient in the home directory of your user account (~) on the server (/home/netid/, where netid is your netID). This folder can take whatever name you like, but we recommend ~/bin or ~/scripts. Or if you want it kind of tucked away, it can be in a hidden folder like ~/.local/bin.

mkdir ~/scripts

Add it to your PATH

The PATH (all caps) is a special group of places visible to your macOS/Linux system at any time and where programs are preferentially invoked from. If you call samtools without specifying an exact path for it, it’s most likely being invoked from a folder in the PATH. POSIX systems like the HPC already have several locations associated with the PATH, and you can add more on a per-user basis. To do that, you need to modify your ~/.bashrc or ~/.zshrc file, depending on whether you use the bash or zsh shells, respectively. Regardless of which of these two you use, the instructions are the same:

Open ~/.bashrc or ~/.zshrc in a terminal editor like nano or vim

nano ~/.bashrc

Towards the top of the config file, add a line with export PATH=<scriptdir>:$PATH, where <scriptdir> is the path to the directory you made in the previous step (e.g., ~/bin, ~/.local/scripts, etc.). The code block below is an example of inserting the export statement into ~/.bashrc, you can ignore the other lines.

export PATH=/programs/julia-1.9.3/bin:$PATH
export PATH=~/.local/bin:$PATH       # <- THIS LINE WAS ADDED

alias cp="cp -i"
alias ls="eza --icons"
alias df='df -h'
...

The next new shell session will incorporate this change. Or, you can force it by asking the shell to reread the config.

source ~/.bashrc

Useful scripts

This is a non-exhaustive list of scripts that might useful to add to your user account. The scripts live in this repository under the scripts/ directory.

disk space by file type

Name: totalsize
Purpose: Lets you get the total amount of disk space occupied by files of a given file type in the current directory.
Dependencies: None
Usage: Automatically searches recursively in the current directory. Limit recursion depth with optional <depth> argument.
```
totalsize .ext <depth>
```
Example:
```
totalsize .vcf
```

Code headers File Storage