Intermediate Shell for Bioinformatics

Lesson	Overview
1. UNIX,Linux & UNIX Shell	Introduction to UNIX operating system, Linux and UNIX Shell
2. UNIX Shell Basics & Recap	Navigating Files & Directories and a review of commands used in routine tasks
3. Download and verify data	Downloading data with wget/curl and check the transferred data’s integrity with check‐sums
4. Streams, Redirection and Pipe	Combining pipes and redirection, Using "Exit" statuses
5. Inspecting and Manipulating Text Data with UNIX Tools - Part 1	Inspect file/s with utilities such as head,less. Extracting and formatting tabular data. Magical grep.
6. Inspecting and Manipulating Text Data with UNIX Tools - Part 2	Substitute matching patterns with sed. Text processing with awk and bioawk
7. Automating File-Processing with find and xargs	Search files by pattern with find and use xargs to execute a command for those objects matching the pattern
8. Puzzles 🧩	Can you use shell scripts to solve these "real" life challenged in molecular biology ?
9. Supplementary_1	Escaping, Special Characters

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Attribution Notice

• This workshop material is heavily inspired by :
  1. Buffalo, V (2015). Bioinformatics Data Skills.O'Reilly Media, Inc
  2. The Carpentries. The Unix Shell . https://swcarpentry.github.io/shell-novice/
  3. The Carpentries. Introduction to Command Line for Genomics. https://datacarpentry.org/shell-genomics/
  4. Rosalind Project. https://rosalind.info/about/

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License

Genomics Aotearoa / New Zealand eScience Infrastructure "Intermediate-Advanced Shell for Bioinformatics" is licensed under the GNU General Public License v3.0, 29 June 2007 . (Follow this link for more information)

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Setup

If possible, we do recommend using the Remote option over Local ( Especially for Windows hosts). This will eliminate the need to install any additional applications

• Remote option will require an existing NeSI Account

Remote

Log into NeSI Mahuika Jupyter Service

1. Follow https://jupyter.nesi.org.nz/hub/login

2. Enter NeSI username, HPC password and 6 digit second factor token
   

3. Choose server options as below
   >>make sure to choose the correct project code nesi02659, number of CPUs CPUs=4, memory 8 GB prior to pressing button.

Local

Local host setup - Windows, MacOS & Linux

Windows HostsMacOSLinux

• Install either
• Git for Windows from https://git-scm.com/download/win OR
• MobaXterm Home (Portable or Installer edition) from https://mobaxterm.mobatek.net/download-home-edition.html
  • Portable edition does not require administrative privileges

• Native terminal client is sufficient.
• It might not comes with wget download data via command line (can be installed with $ brew install wget)
• However, it is not required as we provide a direct link to download data in .zip format

• Native terminal client is sufficient.

bioawk install on all hosts

One of the tools used in this workshop is bioawk which is not a native Linu/UNIX utility. Installing it on MacOS and Linux can be done with $ brew install bioawk & $ sudo apt install bioawk, respectively. Windows hosts might have to do it via conda according to these instructions. However, this will require a prior install of Anaconda Or Miniconda