Linux/Unix and Command Line
Introduction to Linux
- YCRC Workshop: Practical Introduction to Linux, (Video) *Recommended
- Most Commonly Used Commands - RedHat.com
- Command Line for Beginners - Ubuntu.com
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 is tool for searching command line output or files for a certain string (phrase) or regular expression.
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)
- Connecting to the Yale clusters
- Transfer files to/from the cluster
- Advanced SSH configuration
- In-depth guide to
Bashrc and Bash Profiles
- What is the
- [Set aliases for commonly used commands]
- [Environment variables]
tar or tar.gz archive
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 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" means you have two separate installations for Windows and Linux, respectively, that switch between by restarting your computer.
Intro to Python
Parallel Programming with Python
- Quick Tutorial: Python Multiprocessing
- Parallel Programming with Python
- YCRC Workshop: Parallel Python
Intro to R
foreach + dompi
Singularity / Apptainer
Singularity has officially been renamed Apptainer, but we expect no changes to its functionality.
- YCRC Workshop: Containers
- NIH tutorial on Singularity
- NVIDIA tutorial for using GPUs with Singularity