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Online Tutorials

Linux/Unix and Command Line

Introduction to Linux

Note: You can learn more about most commands you come across by typing "man [command]" into the terminal.

awk (text extraction/parsing)

awk is a tool for parsing text and extracting certain section. It is particularly useful for extracting, and even reordering, columns out of tables in text files.

grep

Grep is tool for searching command line output or files for a certain string (phrase) or regular expression.

sed

sed (Stream EDitor) is a tool for making substitutions in a text file. For example, it can be useful for cleaning (e.g. replace NAN with 0) or reformatting data files. The syntax sed uses for substitutions is common in Linux (for example, the same syntax is used in the VIM text editor).

SSH (connecting to the clusters or other remote linux servers)

Bashrc and Bash Profiles

tar or tar.gz archive

.tar or t.ar.gz are common archive (compressed file) formats. Software and data will frequently be distributed in one of these archive formats. The most common command for opening and extracting the contents of a tar archive is tar xvf archive.tar and, for a tar.gz archive, tar xvzf archive.tar.gz . See the following link(s) for more details on creating tar files and more advanced extraction options.

Install Windows and Linux on the same computer

Windows for Linux

It is possible to run Linux terminals and applications from within a Windows installation using the "Windows Subsystem for Linux".

Dual Boot

"Dual Boot" means you have two separate installations for Windows and Linux, respectively, that switch between by restarting your computer.

Python

Intro to Python

Parallel Programming with Python

mpi4py

R

Intro to R

foreach

foreach + dompi

Matlab

Singularity / Apptainer

Documentation

Singularity has officially been renamed Apptainer, but we expect no changes to its functionality.

Tutorials

Last update: December 16, 2022