Introduction to the command line

This is an introduction to the UNIX (Mac/Linux) command line for absolute beginners. It covers some commands and concepts that are widely used in the UNIX command line. Examples are provided throughout. It is recommend that you try out commands as you read about them in your own UNIX system, as well as the exercise towards the end of the page.

If you are using Windows, please see these pages with instructions on installing Ubuntu (a UNIX operating system):

Opening the terminal
The working directory
Cloning the bioinfo-notebook project into your home directory
Changing working directories
Comments and broken lines
Listing directory content with the ls command
Relative paths
Making directories with mkdir
Removing files and directories with the rm command
Using the head command
The tail command
Using the --help argument
Downloading files with wget
Moving and copying with mv and cp
Running the Linux setup shell script
- Video demonstration
Exercise
See also

Opening the terminal

Once you are using a UNIX operating system (i.e. a Mac system, a Linux system, or Ubuntu through either a virtual machine or a Linux subsystem on a Windows machine) open the terminal to use the command line. The terminal is the window in which the command line runs.

If you are using a Mac, click on Spotlight Search (the magnifying glass icon in the top-right corner of the screen), type “Terminal”, and open the Terminal application.
If you are using the Ubuntu app from the Microsoft Store in Windows 10 (Windows Subsystem for Linux), you are already using the Ubuntu terminal.
If you are using an Ubuntu virtual machine: click on the “Show Applications” button in Ubuntu (the nine dots in the bottom left corner of the screen), click on the “Type to search…” bar at the top of the screen, type “Terminal” and press Enter to open the command line.

The UNIX command line will look like this:

(Your UNIX username)@(Your computer's alias):~$ _

This is called the bash prompt…

Your UNIX username is the your system username.
Your computer’s alias is the name UNIX uses to refer to your computer. This will likely contain the model of your computer (e.g. Latitude-E7270).
The tilde (~) indicates that your home directory is the current working directory. The home directory is located at /home/ followed by your UNIX username.
The dollar sign ($) indicates that the terminal is using the bash shell language.

In examples on this page, ronan@dell:~ $ will be used as an example bash prompt.

The working directory

A directory is the same as a folder on your desktop. If you have a “Pictures” folder on your computer’s desktop, this folder is a directory within the desktop directory: its path is Desktop/Pictures/. The working directory is the directory that the command line is currently using. Any files that you create will be in this directory, and any commands you run will use files in this directory (unless you use a path).

To see the current working directory, type pwd into the command line and press Enter (or Return). This will run the “print working directory” command, which will print the path to the current directory in the terminal. In the context of command line programs, “print” means “display in the terminal”.

ronan@dell:~$ pwd
/home/ronan

Cloning the bioinfo-notebook project into your home directory

We will use the files and directories of the bioinfo-notebook project to demonstrate how to use the command line. This project can be copied into your home directory using the git clone command. The git clone command takes the URL of a GitHub project, and copies all of the files and directories of that project into the working directory. To copy the bioinfo-notebook project into your UNIX system using git clone…

Copy the URL of this project: https://github.com/rnnh/bioinfo-notebook
In the UNIX command line, type git clone. Do not press Enter/Return yet.
Paste the URL of this project into the command line; either by right-clicking the terminal window and selecting Paste in VirtualBox, or just right-clicking the Ubuntu window in WSL.
Once git clone followed by the URL of this project is in the command line, press Enter/Return.

It should look like this…

ronan@dell:~$ git clone https://github.com/rnnh/bioinfo-notebook
Cloning into 'bioinfo-notebook'...
remote: Enumerating objects: 178, done.
remote: Counting objects: 100% (178/178), done.
remote: Compressing objects: 100% (138/138), done.
remote: Total 826 (delta 114), reused 68 (delta 40), pack-reused 648
Receiving objects: 100% (826/826), 409.18 KiB | 2.26 MiB/s, done.
Resolving deltas: 100% (505/505), done.

The directory bioinfo-notebook has now been created in the home directory (/home/ronan/bioinfo-notebook).

Changing working directories

The working directory of the command line can be changed using the cd (change directory) command. Use pwd before and after the cd command to check which directory you have moved from and to. Type cd bioinfo-notebook/ to change the working directory to the bioinfo-notebook/ directory.

ronan@dell:~$ pwd
/home/ronan
ronan@dell:~$ cd bioinfo-notebook/
ronan@dell:~/bioinfo-notebook$ pwd
/home/ronan/bioinfo-notebook

You do not need to type this command out in full, typing cd b and pressing the Tab key should complete this command. Notice that the working directory part of the bash prompt has changed from ~ to ~/bioinfo-notebok.

When you press Tab in the command line, it will try to complete the file or directory name for you. If there are multiple options, these options will be printed in the terminal. If there is only one possible option, this option will be filled in. For example, pressing Tab twice after typing cd D could give the following directories beginning with “D” as options:

ronan@dell:~$ cd D
Desktop/   Documents/ Downloads/

In UNIX, directory names are case-sensitive. This means that ~/downloads/ is a different directory than ~/Downloads/.

The command cd ../ can be used to move to move up one directory, cd ../../ can be used to move up two directories, etc. In this example, moving up one directory from /home/ronan/bioinfo-notebook/data/ changes the working directory to /home/ronan/bioinfo-notebook/. Moving up two directories from /home/ronan/bioinfo-notebook/data/ changes the working directory to /home/ronan/.

ronan@dell:~/bioinfo-notebook/data$ pwd
/home/ronan/bioinfo-notebook/data
ronan@dell:~/bioinfo-notebook/data$ cd ../
ronan@dell:~/bioinfo-notebook$ pwd
/home/ronan/bioinfo-notebook
ronan@dell:~/bioinfo-notebook$ cd data/
ronan@dell:~/bioinfo-notebook/data$ cd ../../
ronan@dell:~$ pwd
/home/ronan

Comments and broken lines

The number sign or hash (#) is used for comments in bash. Comments are used in programming to explain or annotate code; they are not run as code. Anything written after a # symbol in the command line is a comment.

ronan@dell:~/bioinfo-notebook$ pwd # This prints the working directory
/home/ronan/bioinfo-notebook
ronan@dell:~/bioinfo-notebook$ ls # This lists the contents of the directory
assets  _config.yml  data  docs  envs  LICENSE  README.md  scripts  temp

Long lines of code can be hard to read. For legibility, long lines of command line code can be broken up with the backslash (\). The \ characters split lines to make them more readable, they do not affect how the code functions.

ronan@dell:~/bioinfo-notebook/data$ head example_nucleotide_sequence.fasta 
>NC_001133.9 Saccharomyces cerevisiae S288C chromosome I, complete sequence
CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACACATCCTAACA
CTACCCTAACACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTC
CACTCGTTACCCTGTCCCATTCAACCATACCACTCCGAACCACCATCCATCCCTCTACTTACTACCACTC
ACCCACCGTTACCCTCCAATTACCCATATCCAACCCACTGCCACTTACCCTACCATTACCCTACCATCCA
CCATGACCTACTCACCATACTGTTCTTCTACCCACCATATTGAAACGCTAACAAATGATCGTAAATAACA
CACACGTGCTTACCCTACCACTTTATACCACCACCACATGCCATACTCACCCTCACTTGTATACTGATTT
TACGTACGCACACGGATGCTACAGTATATACCATCTCAAACTTACCCTACTCTCAGATTCCACTTCACTC
CATGGCCCATCTCTCACTGAATCAGTACCAAATGCACTCACATCATTATGCACGGCACTTGCCTCAGCGG
TCTATACCCTGTGCCATTTACCCATAACGCCCATCATTATCCACATTTTGATATCTATATCTCATTCGGC
ronan@dell:~/bioinfo-notebook/data$ head \
> example_nucleotide_sequence.fasta 
>NC_001133.9 Saccharomyces cerevisiae S288C chromosome I, complete sequence
CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACACATCCTAACA
CTACCCTAACACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTC
CACTCGTTACCCTGTCCCATTCAACCATACCACTCCGAACCACCATCCATCCCTCTACTTACTACCACTC
ACCCACCGTTACCCTCCAATTACCCATATCCAACCCACTGCCACTTACCCTACCATTACCCTACCATCCA
CCATGACCTACTCACCATACTGTTCTTCTACCCACCATATTGAAACGCTAACAAATGATCGTAAATAACA
CACACGTGCTTACCCTACCACTTTATACCACCACCACATGCCATACTCACCCTCACTTGTATACTGATTT
TACGTACGCACACGGATGCTACAGTATATACCATCTCAAACTTACCCTACTCTCAGATTCCACTTCACTC
CATGGCCCATCTCTCACTGAATCAGTACCAAATGCACTCACATCATTATGCACGGCACTTGCCTCAGCGG
TCTATACCCTGTGCCATTTACCCATAACGCCCATCATTATCCACATTTTGATATCTATATCTCATTCGGC

Listing directory content with the `ls` command

The ls command can be used to list the files and directories within the current working directory. Try using the ls command in the bioinfo-notebook/ directory.

ronan@dell:~/bioinfo-notebook$ ls
assets  _config.yml  data  docs  envs  LICENSE  README.md  scripts  temp

Relative paths

From the bioinfo-notebook/ working directory, all of the files in this project can be accessed using relative paths. Without paths, the program only knows which file or directory to look for in the working directory. With paths, the program knows which file or directory to look for and how to get to it from the working directory.

The ls command can be used to list the content of the bioinfo-notebook/data/ from the bioinfo-notebook/ working directory using ls data/.

ronan@dell:~/bioinfo-notebook$ pwd
/home/ronan/bioinfo-notebook
ronan@dell:~/bioinfo-notebook$ ls data/
example_genome_annotation.gtf  example_nucleotide_sequence.fasta

Making directories with `mkdir`

The command mkdir can be used to create a directory. Here is the –help text for the command mkdir:

ronan@dell:~$ mkdir --help
Usage: mkdir [OPTION]... DIRECTORY...
Create the DIRECTORY(ies), if they do not already exist.

Mandatory arguments to long options are mandatory for short options too.
  -m, --mode=MODE   set file mode (as in chmod), not a=rwx - umask
  -p, --parents     no error if existing, make parent directories as needed
  -v, --verbose     print a message for each created directory
  -Z                   set SELinux security context of each created directory
                         to the default type
      --context[=CTX]  like -Z, or if CTX is specified then set the SELinux
                         or SMACK security context to CTX
      --help     display this help and exit
      --version  output version information and exit

GNU coreutils online help: <http://www.gnu.org/software/coreutils/>
Full documentation at: <http://www.gnu.org/software/coreutils/mkdir>
or available locally via: info '(coreutils) mkdir invocation'

In this example, mkdir is used to create a directory called example, which is located in (and is therefore a subdirectory of) the home directory (~). This is the equivalent of making a new folder within a folder on your desktop.

ronan@dell:~$ clear
ronan@dell:~$ pwd
/home/ronan
ronan@dell:~$ mkdir example
ronan@dell:~$ cd example/
ronan@dell:~/example$ pwd
/home/ronan/example

Removing files and directories with the `rm` command

The rm (remove) command is used to remove files and directories. This command must be used with care, as it is not the same as deleting a file or directory on a desktop. Deleted files on a desktop are moved to a Recycle Bin or Trash folder, and are only permanently deleted once they are removed from this folder. When using the rm command, files and directories are permanently deleted; they cannot be recovered.

Here is the –help text for the rm command:

ronan@dell:~$ rm --help
Usage: rm [OPTION]... [FILE]...
Remove (unlink) the FILE(s).

  -f, --force           ignore nonexistent files and arguments, never prompt
  -i                    prompt before every removal
  -I                    prompt once before removing more than three files, or
                          when removing recursively; less intrusive than -i,
                          while still giving protection against most mistakes
      --interactive[=WHEN]  prompt according to WHEN: never, once (-I), or
                          always (-i); without WHEN, prompt always
      --one-file-system  when removing a hierarchy recursively, skip any
                          directory that is on a file system different from
                          that of the corresponding command line argument
      --no-preserve-root  do not treat '/' specially
      --preserve-root   do not remove '/' (default)
  -r, -R, --recursive   remove directories and their contents recursively
  -d, --dir             remove empty directories
  -v, --verbose         explain what is being done
      --help     display this help and exit
      --version  output version information and exit

By default, rm does not remove directories.  Use the --recursive (-r or -R)
option to remove each listed directory, too, along with all of its contents.

To remove a file whose name starts with a '-', for example '-foo',
use one of these commands:
  rm -- -foo

  rm ./-foo

Note that if you use rm to remove a file, it might be possible to recover
some of its contents, given sufficient expertise and/or time.  For greater
assurance that the contents are truly unrecoverable, consider using shred.

GNU coreutils online help: <http://www.gnu.org/software/coreutils/>
Full documentation at: <http://www.gnu.org/software/coreutils/rm>
or available locally via: info '(coreutils) rm invocation'

To remove files, simply type rm followed by the name of the file, and press Enter/Return:

ronan@dell:~/example$ pwd
/home/ronan/example
ronan@dell:~/example$ ls
example_file.txt
ronan@dell:~/example$ rm example_file.txt # Remove the file 'example_file.txt'
ronan@dell:~/example$ ls
ronan@dell:~/example$ 

To remove directories, rm -r must be typed, followed by the name of the directory. Use the rm -r command with caution, as it will permanently delete entire directories and all of their contents. This includes files and other directories within this directory.

In this example, rm -r is used to remove the example/ directory from the home directory:

ronan@dell:~/example$ pwd
/home/ronan/example
ronan@dell:~/example$ cd ../
ronan@dell:~$ pwd
/home/ronan
ronan@dell:~$ rm -r example/
ronan@dell:~$ cd example
bash: cd: example: No such file or directory
ronan@dell:~$ 

Using the `head` command

The head command can be used to view the first part (the head) of a file or files. This command is useful for examining very large files quickly. From the bioinfo-notebook/ working directory, use head data/example_nucleotide_sequence.fasta to view the head of that FASTA file.

ronan@dell:~/bioinfo-notebook$ pwd
/home/ronan/bioinfo-notebook
ronan@dell:~/bioinfo-notebook$ head data/example_nucleotide_sequence.fasta 
>NC_001133.9 Saccharomyces cerevisiae S288C chromosome I, complete sequence
CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACACATCCTAACA
CTACCCTAACACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTC
CACTCGTTACCCTGTCCCATTCAACCATACCACTCCGAACCACCATCCATCCCTCTACTTACTACCACTC
ACCCACCGTTACCCTCCAATTACCCATATCCAACCCACTGCCACTTACCCTACCATTACCCTACCATCCA
CCATGACCTACTCACCATACTGTTCTTCTACCCACCATATTGAAACGCTAACAAATGATCGTAAATAACA
CACACGTGCTTACCCTACCACTTTATACCACCACCACATGCCATACTCACCCTCACTTGTATACTGATTT
TACGTACGCACACGGATGCTACAGTATATACCATCTCAAACTTACCCTACTCTCAGATTCCACTTCACTC
CATGGCCCATCTCTCACTGAATCAGTACCAAATGCACTCACATCATTATGCACGGCACTTGCCTCAGCGG
TCTATACCCTGTGCCATTTACCCATAACGCCCATCATTATCCACATTTTGATATCTATATCTCATTCGGC

The head command takes optional arguments. Command line arguments are extra instructions given to a program when it runs. One of the arguments that can be given to head is -n, which specifies how many lines we want to print per file. The command head -n 5 data/example_nucleotide_sequence.fasta prints the first 5 lines of the file example_nucleotide_sequence.fasta.

ronan@dell:~/bioinfo-notebook$ pwd
/home/ronan/bioinfo-notebook
ronan@dell:~/bioinfo-notebook$ head -n 5 data/example_nucleotide_sequence.fasta
>NC_001133.9 Saccharomyces cerevisiae S288C chromosome I, complete sequence
CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACACATCCTAACA
CTACCCTAACACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTC
CACTCGTTACCCTGTCCCATTCAACCATACCACTCCGAACCACCATCCATCCCTCTACTTACTACCACTC
ACCCACCGTTACCCTCCAATTACCCATATCCAACCCACTGCCACTTACCCTACCATTACCCTACCATCCA

In the UNIX terminal, an asterisk (*) acts as a wildcard. This means that any files or directories that can replace this character will replace it. For example, the bioinfo-notebook/data/ directory contains two files: example_genome_annotation.gtf and example_nucleotide_sequence.fasta. Using the command head -n 5 data/* will print the first 5 lines of both of these files.

ronan@dell:~/bioinfo-notebook$ pwd
/home/ronan/bioinfo-notebook
ronan@dell:~/bioinfo-notebook$ head -n 5 data/*
==> data/example_genome_annotation.gtf <==
#gtf-version 2.2
#!genome-build R64
#!genome-build-accession NCBI_Assembly:GCF_000146045.2
#!annotation-source SGD R64-2-1
NC_001133.9	RefSeq	gene	1807	2169	.	-	.	gene_id "YAL068C"; db_xref "GeneID:851229"; gbkey "Gene"; gene "PAU8"; gene_biotype "protein_coding"; locus_tag "YAL068C"; partial "true"; 

==> data/example_nucleotide_sequence.fasta <==
>NC_001133.9 Saccharomyces cerevisiae S288C chromosome I, complete sequence
CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACACATCCTAACA
CTACCCTAACACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTC
CACTCGTTACCCTGTCCCATTCAACCATACCACTCCGAACCACCATCCATCCCTCTACTTACTACCACTC
ACCCACCGTTACCCTCCAATTACCCATATCCAACCCACTGCCACTTACCCTACCATTACCCTACCATCCA

The asterisk command is especially useful for selecting files with the same file extension. The file extension is the part of the filename after the full stop that specifies the file type: for example, a file ending in .txt is a text file. In a directory with many text files, *.txt selects all of the text files.

The `tail` command

The tail command is the equivalent of the command head, but prints the last part of files instead. This is useful for quickly examining the information at the ends of files.

ronan@dell:~/bioinfo-notebook$ pwd
/home/ronan/bioinfo-notebook
ronan@dell:~/bioinfo-notebook$ tail -n 5 data/*
==> data/example_genome_annotation.gtf <==
NC_001133.9	RefSeq	exon	225460	226863	.	+	.	gene_id "YAR071W"; transcript_id "NM_001178239.1"; db_xref "GeneID:851299"; gbkey "mRNA"; gene "PHO11"; locus_tag "YAR071W"; partial "true"; product "acid phosphatase PHO11"; exon_number "1"; 
NC_001133.9	RefSeq	CDS	225460	226860	.	+	0	gene_id "YAR071W"; transcript_id "NM_001178239.1"; db_xref "SGD:S000000094"; db_xref "GeneID:851299"; experiment "EXISTENCE:direct assay:GO:0003993 acid phosphatase activity [PMID:8817921]"; gbkey "CDS"; gene "PHO11"; locus_tag "YAR071W"; note "One of three repressible acid phosphatases; glycoprotein that is transported to the cell surface by the secretory pathway; induced by phosphate starvation and coordinately regulated by PHO4 and PHO2; PHO11 has a paralog, PHO12, that arose from a segmental duplication"; product "acid phosphatase PHO11"; protein_id "NP_009434.1"; exon_number "1"; 
NC_001133.9	RefSeq	start_codon	225460	225462	.	+	0	gene_id "YAR071W"; transcript_id "NM_001178239.1"; db_xref "SGD:S000000094"; db_xref "GeneID:851299"; experiment "EXISTENCE:direct assay:GO:0003993 acid phosphatase activity [PMID:8817921]"; gbkey "CDS"; gene "PHO11"; locus_tag "YAR071W"; note "One of three repressible acid phosphatases; glycoprotein that is transported to the cell surface by the secretory pathway; induced by phosphate starvation and coordinately regulated by PHO4 and PHO2; PHO11 has a paralog, PHO12, that arose from a segmental duplication"; product "acid phosphatase PHO11"; protein_id "NP_009434.1"; exon_number "1"; 
NC_001133.9	RefSeq	stop_codon	226861	226863	.	+	0	gene_id "YAR071W"; transcript_id "NM_001178239.1"; db_xref "SGD:S000000094"; db_xref "GeneID:851299"; experiment "EXISTENCE:direct assay:GO:0003993 acid phosphatase activity [PMID:8817921]"; gbkey "CDS"; gene "PHO11"; locus_tag "YAR071W"; note "One of three repressible acid phosphatases; glycoprotein that is transported to the cell surface by the secretory pathway; induced by phosphate starvation and coordinately regulated by PHO4 and PHO2; PHO11 has a paralog, PHO12, that arose from a segmental duplication"; product "acid phosphatase PHO11"; protein_id "NP_009434.1"; exon_number "1"; 
###

==> data/example_nucleotide_sequence.fasta <==
GTGTGGTGATGGATAGTGAGTGGATAGTGAGTGGATGGATGGTGGAGTGGGGGAATGAGACAGGGCATGG
GGTGGTGAGGTAAGTGCCGTGGATTGTGATGATGGAGAGGGAGGGTAGTTGACATGGAGTTAGAATTGGG
TCAGTGTTAGTGTTAGTGTTAGTATTAGGGTGTGGTGTGTGGGTGTGGTGTGGGTGTGGGTGTGGGTGTG
GGTGTGGGTGTGGGTGTGGTGTGGTGTGTGGGTGTGGTGTGGGTGTGGTGTGTGTGGG

Using the `--help` argument

For a lot of command line programs, using the command with the --help (or -h) argument will display a short help message on how that command is used.

ronan@dell:~$ head --help
Usage: head [OPTION]... [FILE]...
Print the first 10 lines of each FILE to standard output.
With more than one FILE, precede each with a header giving the file name.

With no FILE, or when FILE is -, read standard input.

Mandatory arguments to long options are mandatory for short options too.
  -c, --bytes=[-]NUM       print the first NUM bytes of each file;
                             with the leading '-', print all but the last
                             NUM bytes of each file
  -n, --lines=[-]NUM       print the first NUM lines instead of the first 10;
                             with the leading '-', print all but the last
                             NUM lines of each file
  -q, --quiet, --silent    never print headers giving file names
  -v, --verbose            always print headers giving file names
  -z, --zero-terminated    line delimiter is NUL, not newline
      --help     display this help and exit
      --version  output version information and exit

NUM may have a multiplier suffix:
b 512, kB 1000, K 1024, MB 1000*1000, M 1024*1024,
GB 1000*1000*1000, G 1024*1024*1024, and so on for T, P, E, Z, Y.

GNU coreutils online help: <http://www.gnu.org/software/coreutils/>
Full documentation at: <http://www.gnu.org/software/coreutils/head>
or available locally via: info '(coreutils) head invocation'

For more in-depth help with a command, the man (manual) command is useful, if it is available. This will open a manual for the program within the terminal. The Up and Down arrow keys (or j and k) can be used to scroll through these manuals, and q is used to exit.

ronan@dell:~$ man head

HEAD(1)                          User Commands                         HEAD(1)

NAME
       head - output the first part of files

SYNOPSIS
       head [OPTION]... [FILE]...

DESCRIPTION
...
 Manual page head(1) line 1 (press h for help or q to quit)

Downloading files with `wget`

The wget command can be used to download files from the directory using the command line. It can take a URL as an argument, and download the file found at that URL into the working directory.

In this example, wget is used to download the amino acid sequence of haemoglobin subunit alpha from UniProt:

ronan@dell:~/bioinfo-notebook$ pwd
/home/ronan/bioinfo-notebook
ronan@dell:~/bioinfo-notebook$ wget \
> https://www.uniprot.org/uniprot/P69905.fasta
--2020-04-15 16:52:27--  https://www.uniprot.org/uniprot/P69905.fasta
Resolving www.uniprot.org (www.uniprot.org)... 128.175.245.202, 193.62.192.81
Connecting to www.uniprot.org (www.uniprot.org)|128.175.245.202|:443... connected.
HTTP request sent, awaiting response... 200 
Length: 233 [text/plain]
Saving to: ‘P69905.fasta’

P69905.fasta        100%[===================>]     233  --.-KB/s    in 0s      

2020-04-15 16:52:28 (7.91 MB/s) - ‘P69905.fasta’ saved [233/233]

ronan@dell:~/bioinfo-notebook$ head P69905.fasta # Examining the start of the downloaded file 
>sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Homo sapiens OX=9606 GN=HBA1 PE=1 SV=2
MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG
KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP
AVHASLDKFLASVSTVLTSKYR

Moving and copying with `mv` and `cp`

The mv and cp commands can be used to move and copy files or directories from the command line. Both of these commands take a target file/directory and a destination file/directory as arguments. The cp commands creates a copy of a file/directory, whereas mv moves it to a new destination. The mv command can be used to rename files, by moving it to the same directory, but with a new file name.

ronan@dell:~/bioinfo-notebook$ mv P69905.fasta data/ # Moving the P69905.fasta file to the data/ directory

ronan@dell:~/bioinfo-notebook$ cd data/ # Changing directory to data/

ronan@dell:~/bioinfo-notebook/data$ ls # Listing files in data/ to confirm that the FASTA file has been moved
example_genome_annotation.gtf      P69905.fasta
example_nucleotide_sequence.fasta  S_cere_GCF_000146045.2_R64_genomic.fna

ronan@dell:~/bioinfo-notebook/data$ mv P69905.fasta haem.fasta # Using mv to rename the FASTA file to haem.fasta

ronan@dell:~/bioinfo-notebook/data$ ls # Listing the files in the directory
example_genome_annotation.gtf      haem.fasta
example_nucleotide_sequence.fasta  S_cere_GCF_000146045.2_R64_genomic.fna

ronan@dell:~/bioinfo-notebook/data$ cp haem.fasta ../ # Creating a copy of haem.fasta in the directory above data/, i.e. the bioinfo-notebook/ directory

ronan@dell:~/bioinfo-notebook/data$ ls # Listing the files in the directory
example_genome_annotation.gtf      haem.fasta
example_nucleotide_sequence.fasta  S_cere_GCF_000146045.2_R64_genomic.fna

ronan@dell:~/bioinfo-notebook/data$ cd ../ # Changing directory to bioinfo-notebook/

ronan@dell:~/bioinfo-notebook$ ls # Listing the files in the directory
assets       data  envs        LICENSE    scripts
_config.yml  docs  haem.fasta  README.md  temp

Running the Linux setup shell script

A shell script can be used to run commands sequentially, without having to input them individually into the command line. One of the shell scripts (ending in .sh) included in this project is scripts/linux_setup.sh. This script downloads and installs conda and the bioinfo-notebook conda environment. This is a quick way to install command line programs discussed in this project, e.g. bowtie2, featureCounts and SAMtools.

A bash shell script can be run using bash followed by a relative path to the script. The shell script linux_setup.sh also includes help text, which can be accessed with the --help or -h argument.

ronan@dell:~/bioinfo-notebook$ pwd
/home/ronan/bioinfo-notebook
ronan@dell:~/bioinfo-notebook$ bash scripts/linux_setup.sh --help
linux_setup.sh 
 
 This script downloads and installs Miniconda3, and uses conda to install 
 the 'bioinfo-notebook' virtual environment. 
 
 Before running this script... 
 
 	 1. Please run the following command: 
 	 	 $ sudo apt-get update 
 	 This will ensure that the software installed will be up-to-date. 
 
 	 2. Please ensure that the 'bioinfo-notebook/' directory is in your 
 	 home directory (~). The path to this directory should look like this: 
 	 	 /home/ronan/bioinfo-notebook 
 
 The 'bash' command is used to run this script: 
 	 $ bash scripts/linux_setup.sh 
 
 Optional arguments: 
 	 -h | --help	 show this help text and exit

Video demonstration

In this demonstration, the bioinfo-notebook GitHub project (also known as a repository or repo) is cloned into the home directory of the UNIX system (in this case, the UNIX system used is Ubuntu). This means that all the files for this project will be downloaded from GitHub into the ~/bioinfo-notebook/ directory. A GitHub repo can be cloned using the command $ git clone followed by the URL of the target repo (which can be found on GitHub using the “Clone or download” button). The Linux setup script is then run from this cloned GitHub repo.

Exercise

Look at the structure of the bioinfo-notebook repository. This outlines how this repository (another term for a GitHub project folder) is structured: it outlines which files and directories are in this project. Most of the files in this project are within subdirectories of the bioinfo-notebook/ directory.

Once you have read this page, and copied this project to your UNIX system, try the following small tasks. These tasks only require one command each.

Change the working directory from bioinfo-notebook/ to bioinfo-notebook/data/.
Change the working directory from bioinfo-notebook/data to bioinfo-notebook/docs, using ../ in your command.
List the files in the bioinfo-notebook/docs/ directory.
Select a file in the bioinfo-notebook/docs/ directory, and display the first 6 lines of it using the head command.
Display the last 2 lines of all the files in the bioinfo-notebook/docs/ directory, using the tail command.
From the bioinfo-notebook/docs/ directory, list the files in the bioinfo-notebook/envs/ directory.

Solutions to this exercise.

Introduction to the command line

Contents

Opening the terminal

The working directory

Cloning the bioinfo-notebook project into your home directory

Changing working directories

Comments and broken lines

Listing directory content with the ls command

Relative paths

Making directories with mkdir

Removing files and directories with the rm command

Using the head command

The tail command

Using the --help argument

Downloading files with wget

Moving and copying with mv and cp