Introduction to the Command-line Interface (CLI)

aka Introduction to Linux Shell

Getting into the Terminal or Command Prompt

For Mac users:

Type "Command + Spacebar" or click on the Spotlight magnifying glass in the upper right-hand corner.
Type "Terminal"
Hit "Return"

You should see something like this:

For Windows users:

In the search bar in the lower left-hand corner, type "cmd"
Hit "Enter"

You should see somethign like this:

Finding out where you are:

Displays your location in the file system

pwd     # pwd (Linux)
chdir   # chdir (Windows)



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# To run these commands in the Jupyter Notebook, preceed with a exclamation mark (!)

!pwd









    



/Users/squiresrb/Documents/version_control/BIOF309-2016-Fall/Week_03

Creates a directory

mkdir   # mkdir directory
mkdir   # mkdir directory



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!mkdir test



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!ls









    



Week03 - 01 - Introduction to the Command-line.ipynb
Week03 - 02 - Week 2 Homework Review.ipynb
Week03 - 03 - Working with Files.ipynb
Week03 - 04 - Homework.ipynb
test

Changes directories with a specified path (absolute path)

cd pathname    # cd /directory/directory
cd pathname    # cd C:/directory/directory



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!cd test

Changes directories with a relative path

cd ..   # cd ..
cd..    # cd..



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!pwd









    



/Users/squiresrb/Documents/version_control/BIOF309-2016-Fall/Week_03



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Absolute Paths versus Relative Paths

Absolute paths start at the root directory in Linux and at the Hard drive Letter in Windows:

/Users/username/Document/BIOF309/file.txt

C:/Users/username/Documents/BIOF309/file.txt

Relative paths are "relative" to the programs currentl location.

A file in the same directory can be prefaced with "./" in linux but Jupyter Notebook does not require it

.\file.txt    # Current directory

Working with files

Lists files

ls     # ls
dir    # dir

Create a file

nano   # nano hello.txt
dir >     # dir > hello.txt

Copies files

cp     # cp thisfile.txt /home/thisdirectory
copy   # copy thisfile.txt C:/Users/thisdirectory



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Moves files

mv    # mv thisfile.txt /home/thisdirectory
move  # move thisfile.txt C:/Users/thisdirectory



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Deletes files

rm    # rm thisfile.txt
del   # rm thisfile.txt



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Compares the contents of files

diff  # diff file1 file2
fc    # diff file1 file2



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Finds a string of text in a file

grep    # grep word or phrase thisfile.txt
find    # grep word or phrase thisfile.txt



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Views contents of a file

less    # less thisfile.txt
more    # less thisfile.txt

To get out type "q"



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Renames a file

mv     # mv thisfile.txt thatfile.txt
ren    # ren thisfile.txt thatfile.txt



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