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  • The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility
  • Computing Resources
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  • Bioinformatics Topics
    • Tools - A Basic Bioinformatics Toolkit
      • Getting more out of Microsoft Excel
      • Bioinformatics Applications of Unix
        • Unix commands applied to bioinformatics
        • Manipulate NGS files using UNIX commands
        • Manipulate alignment files using UNIX commands
      • Alignments and Mappers
      • Relational databases
        • Running Joins on Galaxy
      • Spotfire
    • Tasks - Bioinformatics Methods
      • UCSC Genome Bioinformatics
        • Interacting with the UCSC Genome Browser
        • Obtaining DNA sequence from the UCSC Database
        • Obtaining genomic data from the UCSC database using table browser queries
        • Filtering table browser queries
        • Performing a BLAT search
        • Creating Custom Tracks
        • UCSC Intersection Queries
        • Viewing cross-species alignments
        • Galaxy
          • Intro to Galaxy
          • Galaxy NGS Illumina QC
          • Galaxy NGS Illumina SE Mapping
          • Galaxy SNP Interval Data
        • Editing and annotation gene structures with Argo
      • GeneGO MetaCore
        • GeneGo Introduction
        • Loading Data Into GeneGO
        • Data Management in GeneGO
        • Setting Thresholds and Background Sets
        • Search And Browse Content Tab
        • Workflows and Reports Tab
        • One-click Analysis Tab
        • Building Network for Your Experimental Data
      • Functional Annotation of Gene Lists
      • Multiple Sequence Alignment
        • Clustalw2
      • Phylogenetic analysis
        • Neighbor Joining method in Phylip
      • Microarray data processing with R/Bioconductor
    • Running Jupyter notebooks on luria cluster nodes
  • Data Management
    • Globus
  • Mini Courses
    • Schedule
      • Previous Teaching
    • Introduction to Unix and KI Computational Resources
      • Basic Unix
        • Why Unix?
        • The Unix Tree
        • The Unix Terminal and Shell
        • Anatomy of a Unix Command
        • Basic Unix Commands
        • Output Redirection and Piping
        • Manual Pages
        • Access Rights
        • Unix Text Editors
          • nano
          • vi / vim
          • emacs
        • Shell Scripts
      • Software Installation
        • Module
        • Conda Environment
      • Slurm
    • Introduction to Unix
      • Why Unix?
      • The Unix Filesystem
        • The Unix Tree
        • Network Filesystems
      • The Unix Shell
        • About the Unix Shell
        • Unix Shell Manual Pages
        • Using the Unix Shell
          • Viewing the Unix Tree
          • Traversing the Unix Tree
          • Editing the Unix Tree
          • Searching the Unix Tree
      • Files
        • Viewing File Contents
        • Creating and Editing Files
        • Manipulating Files
        • Symbolic Links
        • File Ownership
          • How Unix File Ownership Works
          • Change File Ownership and Permissions
        • File Transfer (in-progress)
        • File Storage and Compression
      • Getting System Information
      • Writing Scripts
      • Schedule Scripts Using Crontab
    • Advanced Utilization of IGB Computational Resources
      • High Performance Computing Clusters
      • Slurm
        • Checking the Status of Computing Nodes
        • Submitting Jobs / Slurm Scripts
        • Interactive Sessions
      • Package Management
        • The System Package Manager
        • Environment Modules
        • Conda Environments
      • SSH Port Forwarding
        • SSH Port Forwarding Jupyter Notebooks
      • Containerization
        • Docker
          • Docker Installation
          • Running Docker Images
          • Building Docker Images
        • Singularity
          • Differences from Docker
          • Running Images in Singularity
      • Running Nextflow / nf-core Pipelines
    • Python
      • Introduction to Python for Biologists
        • Interactive Python
        • Types
          • Strings
          • Lists
          • Tuples
          • Dictionaries
        • Control Flow
        • Loops
          • For Loops
          • While Loops
        • Control Flows and Loops
        • Storing Programs for Re-use
        • Reading and Writing Files
        • Functions
      • Biopython
        • About Biopython
        • Quick Start
          • Basic Sequence Analyses
          • SeqRecord
          • Sequence IO
          • Exploration of Entrez Databases
        • Example Projects
          • Coronavirus Exploration
          • Translating a eukaryotic FASTA file of CDS entries
        • Further Resources
      • Machine Learning with Python
        • About Machine Learning
        • Hands-On
          • Project Introduction
          • Supervised Approaches
            • The Logistic Regression Model
            • K-Nearest Neighbors
          • Unsupervised Approaches
            • K-Means Clustering
          • Further Resources
      • Data Processing with Python
        • Pandas
          • About Pandas
          • Making DataFrames
          • Inspecting DataFrames
          • Slicing DataFrames
          • Selecting from DataFrames
          • Editing DataFrames
        • Matplotlib
          • About Matplotlib
          • Basic Plotting
          • Advanced Plotting
        • Seaborn
          • About Seaborn
          • Basic Plotting
          • Visualizing Statistics
          • Visualizing Proteomics Data
          • Visualizing RNAseq Data
    • R
      • Intro to R
        • Before We Start
        • Getting to Know R
        • Variables in R
        • Functions in R
        • Data Manipulation
        • Simple Statistics in R
        • Basic Plotting in R
        • Advanced Plotting in R
        • Writing Figures to a File
        • Further Resources
    • Version Control with Git
      • About Version Control
      • Setting up Git
      • Creating a Repository
      • Tracking Changes
        • Exercises
      • Exploring History
        • Exercises
      • Ignoring Things
      • Remotes in Github
      • Collaborating
      • Conflicts
      • Open Science
      • Licensing
      • Citation
      • Hosting
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MIT Resources

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Massachusetts Institute of Technology

On this page
  • Example
  • Options
  • Tab completion
  • History

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  1. Mini Courses
  2. Introduction to Unix and KI Computational Resources
  3. Basic Unix

Anatomy of a Unix Command

A basic UNIX command has 3 parts. These are:

  1. command name

  2. options (zero or more)

  3. arguments (zero or more)

In general, UNIX commands are written as single strings followed by the return key. Note that UNIX commands are case-sensitive, i.e. it does matter whether you type a letter in uppercase or lowercase.

Example

wc –l myfile.txt

The example above has the following components:

  • the command name (wc)

  • one option (-l)

  • one argument (myfile.txt)

Options

  • Also called “switches” or “flags”.

  • Specify the way a given commands must work.

  • Preceded by one or two dashes (one dash if the switch is a single character, two dashes otherwise).

Tab completion

Tab completion is a useful features of UNIX where the shell automatically fills in partially typed commands when the tab key is used. This is advantageous in many ways:

  • Commands or filenames with long or difficult spelling require fewer keystroke to reach

  • In the case of multiple possible completions, the shell will list all filenames beginning with those few characters.

History

Another useful feature is the fact that the shell remembers each typed command, so you can easily recall and run previous commands.

  • By using the up and down arrows at the prompt, you can revisit the command history and recall previously typed commands.

  • Previous commands can be re-executed as they are or can be edited using the left/right arrow.

Use the history command to specify how many and which previous commands to display.

# display last typed commands
history 
#display the last n typed commands
history n
#execute command n
!n
#execute last command in the list
!!
# recall and execute the n-th last command
!-n

Examples:

# recall the last 5 typed commands
history 5 
# recall and execute the 3rd last command
!-3
# recall and execute command number 120
!120
PreviousThe Unix Terminal and ShellNextBasic Unix Commands

Last updated 1 year ago

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