Unix/Linux Crash Course for Computational Biologists
RECETOX Bioinformatics
September 24, 2025
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What is Linux?
• Linux = operating system kernel created in 1991 by Linus Torvalds.
• Inspired by Unix (1970s, AT&T Bell Labs) — designed for multi-user, multitasking
systems.
• Distributed as open-source software under the GNU General Public License
(GPL).
• Most systems we call “Linux” are really GNU/Linux distributions (Ubuntu,
CentOS, Debian, Fedora, etc.).
• Powers servers, smartphones (Android), supercomputers, embedded devices, and
HPC clusters.
• Core philosophy: small, modular tools combined into powerful workflows.
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Tux
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Why Linux for computational biology?
• Ubiquity: Most HPC clusters, cloud VMs, and Docker/Singularity containers run
Linux by default.
• Tool availability: Bioinformatics software (bwa, samtools, STAR, Nextflow,
nf-core) is developed and tested on Linux first.
• Performance: Efficient use of CPU, memory, GPUs, and large storage systems.
• Remote access: Multi-user servers accessed via SSH are all Linux-based; enables
collaborative compute.
• Automation: Shell scripting and command-line tools combine to form
reproducible pipelines.
• Package ecosystems: Conda/mamba (with Bioconda), apt, yum, etc., make
installing software easier.
• Reproducibility and containers: Linux is the base for Docker/Singularity images,
ensuring portable environments.
• Community and support: Tutorials, mailing lists, forums, and shared practices
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Shell and Terminal
• Terminal: where you type. Shell: command interpreter (bash).
• Prompt: user@server: $
Try:
bash --version
echo "Hello, shell!"
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Anatomy of a Linux command
• General structure:
command [options] [arguments]
• Command: the program you are calling (e.g., ls, grep, samtools).
• Options / flags: modify behavior.
• Short: -h, -l, often can be combined (ls -lah).
• Long: –help, –color=auto.
• Arguments: the input(s) for the command (files, patterns, numbers).
• Example:
grep -Rin –include "*.tsv" "pattern" data/
• grep = command
• -Rin and –include "*.tsv" = options
• "pattern" = search term (argument)
• data/ = where to search (argument) 6
Filesystem mental model
• Single tree from /. Home is ˜.
• Hidden files start with dot (e.g., ˜/.bashrc).
• Case-sensitive names.
Explore:
ls /
ls -al ~
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Paths: absolute vs relative
• Absolute: /data/project1/results/
• Relative: results/
• Shortcuts: . (here), .. (parent), ˜ (home)
pwd
cd /mnt/data/unix_linux_crash_course/data
cd ../
cd ~/scratch
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Core navigation & listing
pwd
ls -lah
cd path/to/dir
mkdir newdir
cp source dest
cp -r dirA dirB
mv oldname newname
rm file ; rm -r dir/
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Inspect files
cat file.txt
less file.txt # q quits, /pattern searches
head -n 20 file.txt
tail -n 20 file.txt
tail -f logs/app.log
Bio examples:
zcat data/reads.fastq.gz | head -n 8
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Find things
which bwa
find . -name "*.fastq.gz"
grep "^@" data/reads.fastq
grep -Rin --include "*.tsv" "pattern" .
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Short (-h) vs Long (–help) flags
• Use –help and man to learn options.
command --help
man command
ls -lh --color=auto
cut -f1,3 --delimiter=$'\t' data/table.tsv
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Redirection and pipes
• > overwrite, » append, | pipe.
echo "sample_id\treads" > counts.tsv
wc -l data/*.fastq.gz >> counts.tsv
zcat data/reads.fastq.gz \
| paste - - - - \
| cut -f2 \
| awk '{sum+=length($0)} END {print "bases\t" sum}'
date | tee run.log
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Stdin redirection & globs
sort < data/unsorted.list > sorted.list
ls data/*.fastq.gz
rm data/sample??.tmp
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Variables and quoting
x=42
echo $x
samples="S1 S2 S3"
for s in $samples; do echo $s; done
export PATH=$HOME/bin:$PATH
pattern="^@"
grep "$pattern" data/reads.fastq
date_str=$(date +%Y-%m-%d)
echo "Today is $date_str"
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Permissions (quick peek)
ls -l file
chmod u+x script.sh
chmod g+r data.tsv
chmod o-rwx secret.txt
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Processes & resources
nproc
free -h
df -h
ps -u $USER
top # q to quit
kill 12345
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Remote & transfer
ssh user@server.example.org
scp localfile user@server:~/
rsync -avP data/ user@server:/data/project/
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Mini-exercises
1. Count reads (4 lines/record):
zcat data/reads.fastq.gz | paste - - - - | wc -l
2. Largest 10 FASTQs:
find . -name "*.fastq.gz" -printf '%s\t%p\n' | sort -n | tail -n 10
3. Extract sample IDs from *R1.fastq.gz :
ls data/*_R1.fastq.gz | sed 's/\_R1.fastq.gz//' | sort -u
4. Find "ERROR" in logs and save:
grep -Rin "ERROR" data/logs/ | tee errors.txt
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Cheat sheet
Navigation: pwd, ls -lah, cd, mkdir, cp, mv, rm -r
Inspect: cat, less, head, tail -f, wc -l
Find & filter: find, grep -Rin, cut, sort, uniq, awk, sed
Help: –help, man
Globs: *, ?, [ACGT]
Redirect/pipe: >, », |, tee, <
Vars: x=1, echo $x, export PATH=..., quotes, $()
Processes: nproc, free -h, df -h, ps, top, kill
Remote: ssh, scp, rsync -avP
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Conditions in Bash
if [ -f "data/reads.fastq.gz" ]; then
echo "FASTQ present"
else
echo "File missing!"
fi
• -f : file exists
• -d : directory exists
• -eq, -lt, -gt : numeric tests
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Loops in Bash: for
# Loop through sample IDs
for s in S1 S2 S3; do
echo "Processing $s"
done
# Loop through files
for f in data/*.fastq.gz; do
echo "File: $f"
done
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Loops in Bash: while
n=3
while [ $n -gt 0 ]; do
echo $n
n=$((n-1))
done
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Example: batch processing
for f in data/*.fastq.gz; do
if [ -s "$f" ]; then # check file not empty
echo "QC on $f"
fastqc $f -o results/
else
echo "Skipping $f (empty)"
fi
done
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Conditions & Loops: Quick Reference
Conditions (tests)
-f file file exists
-d dir directory exists
-s file file exists and not empty
-eq, -lt, -gt numeric comparisons
==, != string comparisons
Loops
for var in list; do ...; done iterate over list or files
while [ condition ]; do ...; done repeat until condition fails
Tip: Combine loops + conditions for batch processing (e.g. QC all FASTQs).
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What is a shell script?
• A plain text file with a list of shell commands.
• Lets you automate workflows instead of retyping commands.
• Run as a program after making it executable.
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Writing a Bash script
#!/bin/bash
# myscript.sh - count reads in all FASTQ files
for f in data/*.fastq.gz; do
echo "Counting reads in $f"
n=$(zcat $f | wc -l)
echo "$f has $((n/4)) reads"
done
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Running a Bash script
# Make it executable (once)
chmod +x myscript.sh
# Run with relative or absolute path
./myscript.sh
• Always include the shebang line (#!/bin/bash) at the top.
• Can also run with bash myscript.sh.
• Keep scripts in $HOME/bin or project folder.
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Best practices for scripts
• Start with #!/bin/bash (or #!/usr/bin/env bash).
• Comment your code with #.
• Use variables for filenames and parameters.
• Use loops + conditions to process many files.
• Store scripts under version control (git).
• Share with colleagues for reproducible workflows.
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