Topic: Introduction to Linux Date: September 11 2025 Presentation Slides and Training Materials: Learn more at 00:00:00 Welcome and Introduction to Linux/Bash Shell 00:00:49 How to Access the Shell (Open OnDemand & AGOT) 00:03:36 Course Material and Available Resources 00:06:46 What is Linux? (Operating Systems and MSI's Rocky Linux) 00:08:38 Command Line Interface (CLI) vs. Graphical User Interface (GUI) 00:11:40 Essential Command: `pwd` (Print Working Directory) 00:13:58 Essential Command: `ls` (List Directory Contents) 00:17:15 Essential Command: `cd` (Change Directory) 00:20:15 Getting the Tutorial Files (`curl` and `unzip`) 00:23:40 Essential Command: `ls -l` (Long Format List) 00:28:44 Essential Command: `ls -F` (Classify Output: Files vs. Directories) 00:32:08 Understanding Command Options and Arguments 00:34:02 Navigating with Relative Paths (`..`, `.`, `~`) 00:41:29 Viewing File Contents (`cat`, `less`) 00:47:04 Viewing File Contents: `head` (Start of File) 00:48:29 Viewing File Contents: `tail` (End of File) 00:53:50 Navigating with Absolute Paths (Starting from Root) 00:57:33 Productivity Tip: **Tab Completion** 01:03:08 Essential Command: Creating Directories (`mkdir`) 01:06:50 Essential Command: Creating Files (`touch`) 01:08:42 Essential Command: Editing Files (`nano` Text Editor) 01:11:37 Essential Command: Moving/Renaming Files (`mv`) 01:14:52 Essential Command: Copying Files (`cp`) 01:17:35 Essential Command: Removing Files (`rm`) 01:19:10 Essential Command: Removing Directories (`rm -r` - **CAUTION**) 01:23:29 Using **Wildcards** (`*` and `?`) for Pattern Matching 01:28:41 Wildcard Gotchas (Escaping Special Characters) 01:32:27 **File Permissions** (`chmod`) 01:40:54 Connecting Programs with **Pipes** (`|`) 01:47:04 Combining Tools: Finding the Smallest File (`wc`, `sort`, `head`) 01:54:19 Reordering Data with Pipes (`cut`) 01:58:30 Combining Tools: Extracting Specific Lines (`head` and `tail`) 02:04:16 **Loops** for Automation (`for` loop introduction) 02:11:58 Loops Example: Extracting Classifications from Multiple Files 02:26:08 Revisiting Commands with the **History** Tool 02:30:54 Connecting History with Pipes (`history | tail`) 02:35:10 **Shell Scripts** (Introduction) 02:40:02 Making Scripts Flexible (Using $1 for arguments) 02:44:27 Making Scripts More Flexible (Using $2 and $3 for line numbers) 02:50:39 Shell Script Example: Redoing an Analysis 02:54:21 Finding Things in Files: The **`grep`** Command 03:03:52 `grep` Options (`-c` for count, `-h` for no file names) 03:08:48 Finding Files: The **`find`** Command 03:10:48 `find` with `-name` and `-type d` (directories) 03:13:35 `find` with `-exec` (Executing Commands on Found Files) 03:22:38 **Modules** (MSI Software Management) 03:23:46 `module avail` (See available software) 03:26:15 `module load` (Load software environment) 03:31:02 `module list` (See loaded modules) 03:32:00 `module show` (Get module details) 03:41:00 Introduction to **Slurm** (Scheduler for HPC) 03:42:07 Slurm Monitoring Commands (`sinfo` and `squeue`) 03:43:03 Submitting a Job (`sbatch`) 03:46:17 MSI Resources and Final Contact Information 03:48:35 Review of Module Commands and Conclusion