Introduction to Unix command line.

1. What is the Unix command line?

The Unix command line is a text-based way to control a computer. You type commands into a terminal, and the shell interprets those commands. On Linux servers, HPC clusters and many bioinformatics workstations, the command line is the main interface for running analyses.

2. Terminal, shell and prompt

When you open a terminal, you usually see a prompt. The prompt may show your username, computer name, current directory and a symbol such as $. You type commands after the prompt and press Enter.

andrey@workstation:~/projects$ pwd
/home/andrey/projects

3. Filesystem and paths

Unix-like systems organize files in a tree. The top of the tree is the root directory, written as /. Your personal files are usually in your home directory, for example /home/username on Linux or /Users/username on macOS.

/                 # root directory
/home/username    # user home directory on Linux
/Users/username   # user home directory on macOS
/tmp              # temporary files
/mnt              # mounted disks or network locations on many Linux systems
/project          # project storage on some servers or clusters
/scratch          # temporary high-performance storage on some clusters

4. Navigation: pwd, ls and cd

The first commands to learn are pwd, ls and cd. They show where you are, list files and change directories.

pwd
ls
ls -lh
ls -la
cd ~
mkdir -p unix_tutorial
cd unix_tutorial
pwd

5. Creating, copying, moving and deleting files

File operations are powerful and sometimes irreversible. Learn them carefully on test files before using them on real data.

6. Viewing and summarizing text files

Many scientific files are plain text or compressed text: FASTQ, FASTA, SAM, VCF, GTF, BED, CSV and TSV. Unix commands let you inspect them quickly.

cat > samples.tsv << 'EOF'
sample_id	group	batch
S1	control	A
S2	control	A
S3	treated	B
S4	treated	B
EOF

cat samples.tsv
head -n 2 samples.tsv
wc -l samples.tsv

7. Wildcards, quoting and tab completion

Wildcards help you select many files at once. Quoting protects spaces and special characters from being interpreted by the shell.

8. Pipes and redirection

Pipes and redirection are central Unix ideas. A pipe sends the output of one command into another command. Redirection saves output to a file or reads input from a file.

cut -f 2 samples.tsv
cut -f 2 samples.tsv | sort
cut -f 2 samples.tsv | sort | uniq -c

cut -f 2 samples.tsv | sort | uniq -c > group_counts.txt
cat group_counts.txt

9. Text processing: grep, sort, uniq, cut, awk and sed

Unix text-processing tools are especially useful for logs, metadata tables, genomic intervals and annotation files.

# Show treated samples
grep treated samples.tsv

# Count samples per group
tail -n +2 samples.tsv | cut -f 2 | sort | uniq -c

# Extract sample IDs from batch A
awk 'BEGIN{FS="\t"} NR>1 && $3=="A" {print $1}' samples.tsv

10. Permissions and executable files

Unix permissions control who can read, write or execute a file. Use ls -l to see permissions.

ls -l script.sh

# Example output:
# -rwxr-xr-x 1 user user 120 Jan 01 10:00 script.sh

chmod +x script.sh
./script.sh

11. Processes, jobs and stopping commands

A running command is a process. Long analyses may run for minutes, hours or days. Learn how to monitor and stop commands safely.

12. Working on remote servers

Many bioinformatics analyses run on remote Linux servers or HPC clusters. You usually connect with SSH and transfer files with SCP or rsync.

# Connect to a remote server
ssh username@server.example.org

# Copy one file to the server
scp sample.fastq.gz username@server.example.org:/project/data/

# Copy a folder recursively
scp -r results username@server.example.org:/project/results/

# Synchronize folders efficiently
rsync -avh --progress data/ username@server.example.org:/project/data/

13. PATH, software and help pages

The shell uses the PATH variable to find programs. When you type samtools, the shell searches directories listed in PATH until it finds an executable called samtools.

echo $PATH
which bash
which python
which samtools

bash --version
python --version

man ls
ls --help

14. Writing simple shell scripts

A shell script stores commands in a file so that they can be repeated. Scripts are a major step toward reproducible analysis.

cat > hello_unix.sh << 'EOF'
#!/usr/bin/env bash
set -euo pipefail

echo "Current directory:"
pwd

echo "Files:"
ls -lh
EOF

chmod +x hello_unix.sh
./hello_unix.sh

Good script habits

• Use clear file and folder names.
• Add comments explaining important steps.
• Save scripts in a scripts/ folder.
• Write logs to a logs/ folder.
• Record software versions in the output report.
• Test scripts on small files before running them on full datasets.

15. Command-line examples for bioinformatics

The command line is especially useful for inspecting sequencing files and metadata. The following examples illustrate common operations. Adapt them to your data and tools.

# Show the first FASTQ record from a compressed file
zcat sample_R1.fastq.gz | head -n 4

# Count reads in a compressed FASTQ file
zcat sample_R1.fastq.gz | echo $(( $(wc -l) / 4 ))

ls -lh *.fastq.gz

# Save file sizes to a report
ls -lh *.fastq.gz > fastq_file_sizes.txt

# Show column names
head -n 1 samples.tsv

# Count samples by group
tail -n +2 samples.tsv | cut -f 2 | sort | uniq -c

# Find samples from one batch
awk 'BEGIN{FS="\t"} NR>1 && $3=="batch1" {print $1}' samples.tsv

16. Safe command-line habits

The command line is powerful because it does exactly what you tell it. Develop careful habits from the beginning.

17. Mini exercises

Practice on a safe folder, not on real project data.

mkdir -p ~/unix_practice/{data,results,scripts,logs}
cd ~/unix_practice

cat > data/samples.tsv << 'EOF'
sample_id	group	batch
S1	control	A
S2	control	A
S3	treated	B
S4	treated	B
S5	treated/C	B
EOF

1. Use pwd and ls -lh to inspect the practice folder.
2. Use head and cat to view data/samples.tsv.
3. Use cut, sort and uniq -c to count samples per group.
4. Use grep to find treated samples.
5. Redirect the group counts to results/group_counts.txt.
6. Create a script in scripts/ that repeats the analysis.

18. Beginner Unix command cheat sheet

Official resources and documentation

Use official documentation when you need exact options or advanced behavior for a command.

Frequently asked questions