Introduction to Shell

Episodes

1. UNIX, Linux & UNIX Shell

2. Access the Shell and Introduction to Shell Commands

3. Introduction to Shell Commands - 2

License

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

Attribution Notice

• This workshop material is heavily inspired by :
  1. The Carpentries. The Unix Shell . https://swcarpentry.github.io/shell-novice/
  2. The Carpentries. Introduction to Command Line for Genomics. https://datacarpentry.org/shell-genomics/

Setup

• If possible, we do recommend using the Remote option over Local ( Especially for Windows hosts).

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=2, memory 4 GB prior to pressing button.

Local

Local host setup - Windows, MacOS & Linux

Windows HostsMacOSLinux

• Install,
• 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.

• Native terminal client is sufficient.