Intro to Locus and unix

Training materials for a UNIX introductory course offered on Sept 20th, 2023.

The materials showcase the use of an HPC cluster (LOCUS), yet the code is for general use

• Instructors: Poorani Subramanian (BCBB) and Adam Erck (NIAID High Performance Computing)
• Help Emails: [email protected]
• Class Slides
• Video of lecture"intro to locus...

Class Scripts

handson_unix_I_1.sh
Description: Collection of basic UNIX commands to navigate and move files.

job_script.sh
Description: batch job script for submission with UGE on Locus

Terminal/Shell Software

We will be connecting to Locus via a terminal/shell program. Here are the instructions for finding/installing the appropriate program depending on your OS:

• MacOS: We will use Terminal.app which should already be installed; see How to Open Terminal on Mac for where to find it.
• Windows: We will use PuTTY. To install:
  1. Go to https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html
  2. Scroll down to "Alternative binary files."
  3. Look for putty.exe (the SSH and Telnet client itself).
  4. Click on the blue "putty.exe" link next to 64-bit x86 or 32-bit x86 depending on your computer. If you do not know which version your computer can use, select the 32-bit version. This will download the "putty.exe" executable program.
  5. Look for pscp.exe (an SCP client, i.e. command-line secure file copy).
  6. Click on the blue "pscp.exe" link next to 64-bit x86 or 32-bit x86 depending on your computer. If you do not know which version your computer can use, select the 32-bit version. This will download the "pscp.exe" executable program.
  7. To start PuTTY, navigate to where you downloaded putty.exe, and double click on it. This will open the PuTTY window.
  8. Note: If you install PuTTY this way using the alternative binary file, you should not need administrative privileges. Please feel free to email us (see contact info above) if you have any problems installing.

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Additional Example Scripts and Notes

• Unix Cheat Sheet
  Description: List of the most often-used UNIX commands
• handson_unix_I_2.sh
  Description: Collection of basic UNIX commands for searching plain-test data sets.
• how_to_write_bash_script.sh
  Description: Description of how to write simple script.
• organize.sh
  Description: Example of if-then-else-fi script.
• for_loop.sh
  Description: Example of for loop script.
• for_loop_c.sh
  Description: Example of for loop script in cshell.
• until_loop.sh
  Description: Example of until loop script.
• while_loop.sh
  Description: Example of while loop script.

Past Class Materials

• Lecture: Unix Training (Instructors: Phil Cruz and Amit Roy)
  • Materials of Sept 2019 Unix Training - download
  • Video of lecture: Fundamentals_of_Unix_for_Biologists_subtitled.mp4
• Lecture: Introduction to Awk and Sed programming (Instructor: Amit Roy)
  • Materials Sed Awk code and slides
  • Video: Introduction_to_Awk_and_Sed_programming_(Part I) and Part2

Additional Videos

• Manipulating_files_and_data_on_Linux_MSB7103.subtitled.mp4
• Shell_Scripting_Programming_-_MSB_7103_subtitled.mp4
• Shell_Scripting_Programming_3_23_2021_subtitled_trim.mp4
• Unix_for_Biologists_-Part_1-_11_2022_subtitled.mp4
• Unix_for_Biologists_-Part_2-_11_2022_subtitled.mp4
• Intro_to_Locus_NIAID_High_Performance_Cluster_subtitled.mp4