BCH709 Introduction to Bioinformatics: File Permissions

File Permissions

Linux File Permissions

Watch: Linux File Permissions

See also: File Permission and chmod

In Unix/Linux systems, every file and directory has associated permissions that control who can read, write, or execute them.

Setup: Create Practice Directory

cd ~
mkdir -p permission_practice
cd permission_practice

Understanding Permission Notation

Run ls -l to see permission strings:

-rwxr-xr-x  1  user  group  1234  Jan 20 10:00  filename
│├─┤├─┤├─┤
│ │  │  └── Others permissions (r-x = read + execute)
│ │  └───── Group permissions (r-x = read + execute)
│ └──────── Owner permissions (rwx = read + write + execute)
└────────── File type (- = file, d = directory, l = link)

Permission values:

Step 1: View Default Permissions

touch testfile.txt
ls -l testfile.txt

-rw-r--r-- 1 username group 0 Jan 20 10:00 testfile.txt

The default 644 means: owner can read/write, others can only read.

Step 2: chmod with Numbers

Calculate permissions by adding: r(4) + w(2) + x(1)

Try this: Make a script executable

# Create a test script
echo '#!/bin/bash' > myscript.sh
echo 'echo "Hello from script!"' >> myscript.sh
cat myscript.sh

#!/bin/bash
echo "Hello from script!"

# Try to run it (will fail)
./myscript.sh

bash: ./myscript.sh: Permission denied

# Add execute permission (755 = rwxr-xr-x)
chmod 755 myscript.sh
ls -l myscript.sh

-rwxr-xr-x 1 username group 42 Jan 20 10:00 myscript.sh

# Now run it
./myscript.sh

Hello from script!

Step 3: chmod with Letters

Use: u(user/owner), g(group), o(others), a(all) Operators: +(add), -(remove), =(set exactly)

touch symbolic_test.txt
ls -l symbolic_test.txt

-rw-r--r-- 1 username group 0 Jan 20 10:00 symbolic_test.txt

# Add execute for owner
chmod u+x symbolic_test.txt
ls -l symbolic_test.txt

-rwxr--r-- 1 username group 0 Jan 20 10:00 symbolic_test.txt

# Remove read for others
chmod o-r symbolic_test.txt
ls -l symbolic_test.txt

-rwxr----- 1 username group 0 Jan 20 10:00 symbolic_test.txt

Common Permission Patterns

Challenge: Create a Private Directory

mkdir my_private
chmod 700 my_private
ls -ld my_private

Expected Output

drwx------ 2 username group 4096 Jan 20 10:00 my_private

The d indicates directory. Only owner has rwx access.