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Description Linux Command-Line Cheat Sheet
Authors christine Tranchant-Dubreuil (christine.tranchant@ird.fr)
Creation Date 26/02/2018
Last Modified Date 20/10/2018

Summary


Moving around the Filesystem and manipulating files/folders

Printing the name/full path of the current directory pwd
[tranchant@master0 ~]$ pwd
/home/tranchant

Listing files in a directory ls

ls: list all files in the current directory

[tranchant@master0 ~]$ ls 
AIRAIN
All-EST-coffea.fasta
all-gene.gff3.100000.gene-density
all_no_TE.gff3
all_no_TE.gff3.100000.gene-density
all_no_TE.gff3.10000.gene-density
All-SNP.vcf.density100000.snpden
blast_batch.pl
blast.sh
circos
DEDUP2-1
DEDUP2-all
Desktop
FASTA-TRINITY
fastq-stat.txt
GBS
Listing files in a directory gived as argument ls directory_name
[tranchant@master0 ~]$ ls /home 
abate
abdelrah
adam
adeoti
adereeper
admin
agrondi
aichatou
ls -l : Display the long format listing of all files in the current directory
[tranchant@master0 ~]$ ls -l
total 148272
drwxr-xr-x 10 tranchant ggr      4096 13 mars   2017 AIRAIN
-rwxr-xr-x  1 tranchant ggr  51128305 11 sept. 14:16 All-EST-coffea.fasta
-rw-r--r--  1 tranchant ggr     95117 24 févr.  2017 all-gene.gff3.100000.gene-density
-rwxr-xr-x  1 tranchant ggr  64221458 24 févr.  2017 all_no_TE.gff3
-rw-r--r--  1 tranchant ggr     93796 24 févr.  2017 all_no_TE.gff3.100000.gene-density
-rw-r--r--  1 tranchant ggr    889389 24 févr.  2017 all_no_TE.gff3.10000.gene-density
-rwxr-xr-x  1 tranchant root    90498  5 déc.  07:21 All-SNP.vcf.density100000.snpden
-rwxr-xr-x  1 tranchant ggr     10366 29 mars   2017 blast_batch.pl
-rwxr-xr-x  1 tranchant ggr       878 29 mars   2017 blast.sh
drwxr-xr-x  3 tranchant ggr      4096 19 janv. 15:02 circos
drwxr-sr-x  2 tranchant ggr      4096  8 juin   2017 DEDUP2-1
drwxr-sr-x  2 tranchant ggr      4096  8 juin   2017 DEDUP2-all
drwxr-xr-x  4 root      root     4096  9 juil.  2015 Desktop
drwxr-sr-x  2 tranchant ggr      8192  8 juin   2017 FASTA-TRINITY
-rw-r--r--  1 tranchant ggr      1056 30 nov.  15:31 fastq-stat.txt
drwxr-xr-x  2 tranchant ggr        48 10 août   2016 GBS
ls -a : Display all the files and directories (even hidden files)
[tranchant@master0 ~]$ ls -a
.                                                localConfig.pm
..                                               .localConfig.pm.swp
AIRAIN                                           localConfig-USR.pm
All-EST-coffea.fasta                             LOG
all-gene.gff3.100000.gene-density                .ls_couleur
all_no_TE.gff3                                   .Mathematica
all_no_TE.gff3.100000.gene-density               .matplotlib
all_no_TE.gff3.10000.gene-density                .Megan.def
All-SNP.vcf.density100000.snpden                 Microsatellite_markers
.apollo                                          moduleLoad
.bash_history                                    .mozilla
.bash_logout                                     .oracle_jre_usage
.bash_profile                                    out.sites.pi
.bashrc                                          out.windowed.pi
blast_batch.pl                                   parse-go.pl
blast.sh                                         password.txt
.cache                                           path-new.txt
circos                                           path.sh
.config                                          PATH.sh
.cpan                                            path.txt
Data-TP                                          PERL
.dbus                                            perl5

Moving in the file tree cd

cd DIRECTORY_NAME : change the current working directory to ‘directory’ change directory

[tranchant@master0 ~]$ cd FASTQ

Making directories mkdir directory_name

mkdir directory_name: make a directory in your current working directory type make directory

[tranchant@master0 ~]$ mkdir results

Copying files cp

copy


Moving files mv

move

Be careful : use preferentially cp command rather than mv command to move big files

Removing files and directories using rmand rmdir

remove

rm file_name: delete (remove) a file (here file_name) To delete (remove) a file, use the rm command. As an example, we are going to create a copy of the science.txt file then delete it.

rmdir directory_name : remove a directory (make sure it is empty first because linux will not let remove a non-empty directory).


Displaying the contents of a file on the screen

clear (clear screen) clear

clear : clears the terminal. Before displaying files, it’s possible to clear the terminal window with this command.


Display the content of file using cat

cat file1 : displays the contents of a file on the screen concatenate

cat file1 file2

cat *.fasta


Display the content of file using less

less file_name : writes the contents of a file onto the screen a page at a time. Less is used in preference to cat for long files.


Display the begin of a file using head

head file_name : writes the first ten lines of a file to the screen.

[tranchant@master0 ~]$ head 
head -n 5

Display the end of a file using head

tail file_name : writes the last ten lines of a file to the screen.

[tranchant@master0 ~]$ tail
tail -n 5

Searching the contents of a file

Searching word in a file using grep

grep motif file_name : searches files for specified words or patterns. First clear the screen, then type

To search for a phrase or pattern, you must enclose it in single quotes (the apostrophe symbol). For example to search for spinning top, type

 
# printed out each line containg the word science.

# The grep command is case sensitive; it distinguishes between Science and science.

#To ignore upper/lower case distinctions, use the -i option, i.e. type
[tranchant@master0 ~]$grep -i science science.txt

#
[tranchant@master0 ~]$grep -i 'spinning top' science.txt

Some of the other options of grep are:

-v display those lines that do NOT match -n precede each matching line with the line number -c print only the total count of matched lines

Try some of them and see the different results. Don’t forget, you can use more than one option at a time. For example, the number of lines without the words science or Science is grep -ivc science science.txt


Count for word, line count in a file using wc

wc: short for word count (word count)


Creating and extracting a tar gz archive using tar
 
# compress the contents of source-folder-name to a tar.gz archive named tar-archive-name.tar.gz
[tranchant@master0 ~]$tar -zcvf tar-archive-name.tar.gz source-folder-name 
 
# extract the archive to the folder tar-archive-name. 
tar -zxvf tar-archive-name.tar.gz 

Compressing and extracting files using gzip

Knowing how much space a file or directory is using on a disk with du

du [options] [file or dir]

If you use it with no arguments you will the usage of all files and directories (recursively) of the working directory.

-h : Shows the in human readable format -s : Sumarize, so it displays the total of each subdirectory and not for its contents


A symbolic link, also termed a soft link, is a special kind of file that points to another file, much like a shortcut in Windows or a Macintosh alias.

ln -s source_file myfile

Note :


Downloading a file over HTTP with wget

wget http://website.com/files/file.zip : downloads the file http://website.com/files/file.zip into the working directory.


Find files by name or extension with find

find options path motif_file

The following example search for k64 files in the current directory and all sub-directories:

[durreuic@cobalt172 ~]$find . -name "*k64*" 
./mappingGlabv2/fastqPairedUnmappedBartiivsOmap/TEST/k64ctg-TOGGLEmappingRE
./mappingGlabv2/fastqPairedUnmappedBartiivsOmap/TEST/k64`

License

The resource material is licensed under the Creative Commons Attribution 4.0 International License (here).