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  • The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility
  • Computing Resources
    • Active Data Storage
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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
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        • 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
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      • Conflicts
      • Open Science
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  1. Mini Courses
  2. Introduction to Unix
  3. The Unix Shell
  4. Using the Unix Shell

Editing the Unix Tree

Make sure to run all of the copy commands below, as we'll be using files from the Ostrom server later in the course.

  • mkdir

    • This command name stands for "make a directory".

    • It creates a new folder (or directory). If no path is specified, the new directory is created in the current directory.

# start in your home directory
cd ~

# create a directory named "unixclass"
# with a subdirectory named "testdir"
mkdir unixclass
mkdir unixclass/testdir

# change current directory directly to "testdir"
cd unixclass/testdir 

# go to the parent directory (i.e. unixclass)
# and print the working directory
cd ..
pwd
  • touch

    • This command creates an empty file with the given name.

# Go to /home/<your username>/unixclass
cd ~/unixclass

# Create an empty file named "hello.txt"
touch hello.txt

# List the files in the directory to verify that worked
ls
  • cp and mv

    • These commands stand for "copy" and "move," respectively.

    • They copy / move files and directories to the specified location.

    • Wildcards symbols such as "*" or "?" are commonly used to copy multiple files with a single command.

      • The symbol "*" stands for any number of alphanumeric characters.

      • The symbol "?" stands for a single alphanumeric character.

# Start in ~/unixclass
cd ~/unixclass

# copy the file named arrayDat.txt into your unix_class directory
cp /net/ostrom/data/dropbox/arrayDat.txt .
ls
# copy all the files with suffix "array”
# into the current directory 
cp /net/ostrom/data/dropbox/array* .
ls

# copy any file whose extension is "txt" 
cp /net/ostrom/data/dropbox/*.txt .
ls

# copy all files
cp /net/ostrom/data/dropbox/* .
ls
  • rmdir and rm

    • rmdir only removes empty directories, rm removes both directories and files.

    • rm needs -r flag to remove directories.

# Start in ~/unixclass
cd ~/unixclass

# Create a temporary directory
mkdir trash

# create copies of arrayDat.txt in the temporary directory
cp arrayDat.txt trash/arrayDat1.txt
cp arrayDat.txt trash/arrayDat2.txt
cp arrayDat.txt trash/arrayDat3.txt
cp arrayDat.txt trash/arrayDat4.txt

ls trash
# Try to delete the directory with `rmdir`
rmdir trash

# Try to delete the directory with `rm -r`
rm -r trash
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Last updated 11 months ago

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