learning-linux-winfrednyoroka created by GitHub Classroom
Basic Command lines to navigate the terminal
pwd _it means print working directory, you get the path of where you are in the directory
ls _it means you are listing the items either they could be directories or subdirectopries or they could be files in your directory either the current directory or another directory away from where you are.
list can take up options
ls -l ls-a ls -alh ls -R
cd _it involves changing your directory
type the following: cd _it takes you to your home directory cd ~ _it takes you to home directory cd / _it takes you to root directory
cd . _it refers to your current directory
cd .. _it takes you to one directory back, actually the parent directory of where you are except when in the root directory
cd ../.. _it takes you two levels up from where you are currently
mkdir _ this command enables one to create a directory for instance: mkdir learning_unix
NB: when naming directories in terminal avoid use of spaces, since terminal uses spaces when giving commands. instead make use of underscores
mkdir unixstuff mkdir -p outer_git/inner_git The above command line helps you create two directories at the same time where the second directory is hosted within the first directory and where any of the directories does not exist. it thus creates directories as needed.
mkdir --help
man helps the operator access the manual pages for each unix command e.g
| man | command |
|---|---|
| man | mkdir |
| man | ls |
| man | grep |
| man | cp |
| man | cd |
Remove rm is a very dangerous command you have to use it carefully once deleted you will never recover yourfiles or directories
NB you can only remove a directory when you are outside the directory e.g rmdir inner_git
rmdir index* , remove all files starting with index
rm -i index* -when you use the option -i it asks you whether you really sure you want to delete the file or directory
click tab once its used for autocompletion of file and directory names
touch this command can be used in creating empty files
e.g touch learn_git.txt
mv -this command helps in moving files between directories. however, it does not make a copy of the file.
In moving files then you must specify the file and the directory you want to move to
e.g mv notes.txt unixstuff/
mv *.txt unixstuff/
mv test1 test2
in the above case test 1 and test 2 are directories. we are moving test 1 to test 2
cp _ it involves copying files into directories. the advantage is that you always retain a copy of your original file
cp 'input the file name' "preferred directory"
for instance : cp '~/Documents/NGS/COURSE_DATA/UNIX COURSE/MALARIA.FASTA' "."
mv- can be used in renaming files for instance:
mv inner.txt unixstuff/outer.txt (inner.txt is my old file name while oute.txt is my new file name; unixstuff is thelocation i am moving to and have it in a different name)
1. using the command less use the command less to view the contant of a file per page. this command allows you to view the file but you can never edit the file content Echo this command prints the statement on the screen
e.g echo winfred is my name; it prints this statement on the terminal. however, ECHO can be used to redirect the statement into a file and we can use less command to view the file
e.g echo "winfred is my name" > unixstuff.txt
less unixstuff.txt
echo "introduction to programming" >> unixstuff.txt when we make use of >> we append the statement to the previous unlike when we use > which leads to overwriting the file. 2. using cat when we use cat command it displays all contents of the file of which the operator has no control of until it brings you another prompt. it can be used to combine multiple files and as well can be used to make a copy of the file
cat mal.fasta typ.fasta >combined.fasta cat *.fastq> combined.fastq
cat mal.fasta >mal2.fasta
we can use ls -l which gives us the number of lines and the size of the file in bytes
instead we can use wc which gives us the lines, words and characters wc can take options for instance wc -l which give us the number of lines in the file
wc readme.md wc -l readme.md
we make use of the nano
nano unixstuff.txt
down the terminal it provides the operator with options which we type in using Ctrl + X to mean exit
$PATH envirnment variable echo can to be used in displaying environment variables e.g
echo $USER
echo $PATH
it displays the variables in the environmnt that are directories containing the programs we run like the ls command in the bin