Linux Patcher

Automate Linux server patching and Docker container updates across multiple hosts via SSH.

[WARNING] Important disclaimers

Distribution support status

Fully tested:

• [OK] Ubuntu - Tested end-to-end with real infrastructure

Supported but untested:

• [WARNING] Debian GNU/Linux - Commands based on official documentation
• [WARNING] Amazon Linux - Supports both AL2 (yum) and AL2023 (dnf)
• [WARNING] RHEL (Red Hat Enterprise Linux) - Supports RHEL 7 (yum) and 8+ (dnf)
• [WARNING] AlmaLinux - RHEL-compatible, uses dnf
• [WARNING] Rocky Linux - RHEL-compatible, uses dnf
• [WARNING] CentOS - Supports CentOS 7 (yum) and 8+ (dnf)
• [WARNING] SUSE/OpenSUSE - Uses zypper package manager

Testing Recommendation: Always test untested distributions in a non-production environment first. The script will warn you when running on untested distributions.

Security Notice

This skill requires:

• Passwordless sudo access - Configured with restricted permissions
• SSH key authentication - No passwords stored or transmitted
• PatchMon credentials - Stored securely in user's home directory

Read

SETUP.md

for complete security configuration guide.

Quick Start

Automated (Recommended)

Patch all hosts from PatchMon (automatic detection):

python scripts/patch_cli.py auto
# or: scripts/patch-auto.sh

Skip Docker updates (packages only):

python scripts/patch_cli.py auto --skip-docker

Preview changes (dry-run):

python scripts/patch_cli.py auto --dry-run

Manual (Alternative)

Single host - packages only:

python scripts/patch_cli.py host-only user@hostname
# or: scripts/patch-host-only.sh user@hostname

Single host - full update:

python scripts/patch_cli.py host-full user@hostname /path/to/docker/compose

Multiple hosts from config:

python scripts/patch_cli.py multiple config-file.conf

Features

• PatchMon integration - Automatically detects hosts needing updates
• Smart Docker detection - Auto-detects Docker and Compose paths
• Selective updates - Skip Docker updates with

  --skip-docker

  flag
• Passwordless sudo required - Configure with

  visudo

  or

  /etc/sudoers.d/

  files
• SSH key authentication - No password prompts
• Parallel execution - Update multiple hosts simultaneously
• Dry-run mode - Preview changes without applying
• Manual override - Run updates on specific hosts without PatchMon

Configuration

Option 1: Automatic via PatchMon (Recommended)

Configure PatchMon credentials for automatic host detection:

cp scripts/patchmon-credentials.example.conf ~/.patchmon-credentials.conf
nano ~/.patchmon-credentials.conf

Set your credentials:

PATCHMON_URL=https://patchmon.example.com
PATCHMON_USERNAME=your-username
PATCHMON_PASSWORD=your-password

Then simply run:

scripts/patch-auto.sh

The script will:

1. Query PatchMon for hosts needing updates
2. Auto-detect Docker on each host
3. Apply appropriate updates (host-only or full)

Option 2: Single Host (Quick Manual)

Run scripts directly with command-line arguments (no config file needed).

Option 3: Multiple Hosts (Manual Config)

Create a config file based on

scripts/patch-hosts-config.example.sh

:

cp scripts/patch-hosts-config.example.sh my-servers.conf
nano my-servers.conf

Example config:

# Host definitions: hostname,ssh_user,docker_path
HOSTS=(
  "webserver.example.com,ubuntu,/opt/docker"
  "database.example.com,root,/home/admin/compose"
  "monitor.example.com,docker,/srv/monitoring"
)

# Update mode: "host-only" or "full"
UPDATE_MODE="full"

# Dry run mode (set to "false" to apply changes)
DRY_RUN="true"

Then run:

scripts/patch-multiple.sh my-servers.conf

Prerequisites

Required on control machine (where you run the agent or scripts)

• Shell or agent environment (e.g. terminal, exec tool) to run the patch scripts
• SSH client installed (

  ssh

  command available)
• Bash 4.0 or higher
• curl installed (for PatchMon API)
• jq installed (for JSON parsing)
• PatchMon installed (required to check which hosts need updating)
  • Does NOT need to be on the same host as your agent
  • Can be installed on any server accessible via HTTPS
  • Download: https://github.com/PatchMon/PatchMon

Install missing tools:

# Ubuntu/Debian
sudo apt install curl jq

# RHEL/CentOS/Rocky/Alma
sudo dnf install curl jq

# macOS
brew install curl jq

Required on Target Hosts

• SSH server running and accessible
• SSH key authentication configured (passwordless login)
• Passwordless sudo configured for patching commands (see SETUP.md)
• Docker installed (optional, only for full updates)
• Docker Compose installed (optional, only for full updates)
• PatchMon agent installed and reporting (optional but recommended)

PatchMon Setup (Required for Automatic Mode)

PatchMon is required to automatically detect which hosts need patching.

Important: PatchMon does NOT need to be on the same server as your agent. Install PatchMon on a separate server; your agent (or you) query it via API.

Download PatchMon:

• GitHub: https://github.com/PatchMon/PatchMon
• Documentation: https://docs.patchmon.net

What you need:

• PatchMon server installed on ANY accessible server (not necessarily the agent/control host)
• PatchMon agents installed on all target hosts you want to patch
• PatchMon API credentials (username/password)
• Network connectivity from control/agent host to PatchMon server (HTTPS)

Architecture:

┌─────────────────┐      HTTPS API      ┌─────────────────┐
│ Control / agent │ ──────────────────> │ PatchMon Server │
│ host            │    Query updates    │ (separate host) │
└─────────────────┘                     └─────────────────┘
                                                  │
                                                  │ Reports
                                                  ▼
                                         ┌─────────────────┐
                                         │ Target Hosts    │
                                         │ (with agents)   │
                                         └─────────────────┘

Quick Start:

1. Install PatchMon server on a separate server (see GitHub repo)
2. Install PatchMon agents on all hosts you want to patch
3. Configure the control machine to access PatchMon API:

cp scripts/patchmon-credentials.example.conf ~/.patchmon-credentials.conf
nano ~/.patchmon-credentials.conf  # Set PatchMon server URL
chmod 600 ~/.patchmon-credentials.conf

Detailed setup: See

references/patchmon-setup.md

for complete installation guide.

Can I use this skill without PatchMon? Yes! You can use manual mode to target specific hosts without PatchMon. However, automatic detection of hosts needing updates requires PatchMon.

On Target Hosts

Required:

• SSH server running
• Passwordless sudo for the SSH user (for

  apt

  and

  docker

  commands)
• PatchMon agent installed and reporting (for automatic mode)

For full updates:

• Docker and Docker Compose installed
• Docker Compose files exist at specified paths

Configure Passwordless Sudo

On each target host, create

/etc/sudoers.d/patches

:

# For Ubuntu/Debian systems
username ALL=(ALL) NOPASSWD: /usr/bin/apt, /usr/bin/docker

# For RHEL/CentOS systems
username ALL=(ALL) NOPASSWD: /usr/bin/yum, /usr/bin/docker, /usr/bin/dnf

Replace

username

with your SSH user. Test with

sudo -l

to verify.

Update Modes

Host-Only Updates

Updates system packages only:

• Run

  apt update && apt upgrade

  (or

  yum update

  on RHEL)
• Remove unused packages (

  apt autoremove

  )
• Does NOT touch Docker containers

When to use:

• Hosts without Docker
• Security patches only
• Minimal downtime required

Full Updates

Complete update cycle:

• Update system packages
• Clean Docker cache (

  docker system prune

  )
• Pull latest Docker images
• Recreate containers with new images
• Causes brief service interruption

When to use:

• Docker-based infrastructure
• Regular maintenance windows
• Application updates available

Workflow

Automatic Workflow (patch-auto.sh)

1. Query PatchMon - Fetch hosts needing updates via API
2. For each host:
   • SSH into host
   • Check if Docker is installed
   • Auto-detect Docker Compose path (if not specified)
   • Apply host-only OR full update based on Docker detection
3. Report results - Summary of successful/failed updates

Host-Only Update Process

1. SSH into target host
2. Run

   sudo apt update

3. Run

   sudo apt -y upgrade

4. Run

   sudo apt -y autoremove

5. Report results

Full Update Process

1. SSH into target host
2. Run

   sudo apt update && upgrade && autoremove

3. Navigate to Docker Compose directory
4. Run

   sudo docker system prune -af

   (cleanup)
5. Pull all Docker images listed in compose file
6. Run

   sudo docker compose pull

7. Run

   sudo docker compose up -d

   (recreate containers)
8. Report results

Docker Detection Logic

When using automatic mode:

• Docker installed + compose file found → Full update
• Docker installed + no compose file → Host-only update
• Docker not installed → Host-only update
• --skip-docker flag set → Host-only update (ignores Docker)

Docker Path Auto-Detection

When Docker path is not specified, the script checks these locations:

1. /home/$USER/Docker/docker-compose.yml

2. /opt/docker/docker-compose.yml

3. /srv/docker/docker-compose.yml

4. $HOME/Docker/docker-compose.yml

5. Current directory

Override auto-detection:

scripts/patch-host-full.sh user@host /custom/path

Examples

Example 1: Automatic update via PatchMon (recommended)

# First time: configure credentials
cp scripts/patchmon-credentials.example.conf ~/.patchmon-credentials.conf
nano ~/.patchmon-credentials.conf

# Run automatic updates
scripts/patch-auto.sh

Example 2: Automatic with dry-run

# Preview what would be updated
scripts/patch-auto.sh --dry-run

# Review output, then apply
scripts/patch-auto.sh

Example 3: Skip Docker updates

# Update packages only, even if Docker is detected
scripts/patch-auto.sh --skip-docker

Example 4: Manual single host, packages only

scripts/patch-host-only.sh admin@webserver.example.com

Example 5: Manual single host, full update with custom Docker path

scripts/patch-host-full.sh docker@app.example.com /home/docker/production

Example 6: Manual multiple hosts from config

scripts/patch-multiple.sh production-servers.conf

Example 7: Via your agent or chat

If your platform supports natural language or chat, you can ask (e.g.):

• "Update my servers"
• "Patch all hosts that need updates"
• "Update packages only, skip Docker"

Run the scripts via your platform's command or terminal; use automatic mode (

scripts/patch-auto.sh

) to query PatchMon and report results.

Troubleshooting

PatchMon Integration Issues

"PatchMon credentials not found"

• Create credentials file:

  cp scripts/patchmon-credentials.example.conf ~/.patchmon-credentials.conf

• Edit with your PatchMon URL and credentials
• Or set

  PATCHMON_CONFIG

  environment variable to custom location

"Failed to authenticate with PatchMon"

• Verify PatchMon URL is correct (without trailing slash)
• Check username and password
• Ensure PatchMon server is accessible:

  curl -k https://patchmon.example.com/api/health

• Check firewall rules

"No hosts need updates" but PatchMon shows updates available

• Verify PatchMon agents are running on target hosts:

  systemctl status patchmon-agent

• Check agent reporting intervals:

  /etc/patchmon/config.yml

• Force agent update:

  patchmon-agent report

System Update Issues

"Permission denied" on apt/docker commands

• Configure passwordless sudo (see Prerequisites section)
• Test with:

  ssh user@host sudo apt update

"Connection refused"

• Verify SSH access:

  ssh user@host echo OK

• Check SSH keys are configured
• Verify hostname resolution

Docker Compose not found

• Specify full path:

  scripts/patch-host-full.sh user@host /full/path

• Or install Docker Compose on target host
• Auto-detection searches:

  /home/user/Docker

  ,

  /opt/docker

  ,

  /srv/docker

Containers fail to start after update

• Check logs:

  ssh user@host "docker logs container-name"

• Manually inspect:

  ssh user@host "cd /docker/path && docker compose logs"

• Rollback if needed:

  ssh user@host "cd /docker/path && docker compose down && docker compose up -d"

PatchMon Integration (Optional)

For dashboard monitoring and scheduled patching, see

references/patchmon-setup.md

.

PatchMon provides:

• Web dashboard for update status
• Per-host package tracking
• Security update highlighting
• Update history

Security Considerations

• Passwordless sudo is required for automation
  • Limit to specific commands (

    apt

    ,

    docker

    only)
  • Use

    /etc/sudoers.d/

    files (easier to manage)
• SSH keys should be protected
  • Use passphrase-protected keys when possible
  • Restrict key permissions:

    chmod 600 ~/.ssh/id_rsa

• Review updates before applying in production
  • Use dry-run mode first
  • Test on staging environment
• Schedule updates during maintenance windows
  • Use your platform's scheduler or cron for automation
  • Coordinate with team for Docker updates (brief downtime)

Best Practices

1. Test first - Run dry-run mode before applying changes
2. Stagger updates - Don't update all hosts simultaneously (avoid full outage)
3. Monitor logs - Check output for errors after updates
4. Backup configs - Keep Docker Compose files in version control
5. Schedule wisely - Update during low-traffic windows
6. Document paths - Maintain config files for infrastructure
7. Reboot when needed - Kernel updates require reboots (not automated)

Reboot Management

The scripts do NOT automatically reboot hosts. After updates:

1. Check if reboot required:

   ssh user@host "[ -f /var/run/reboot-required ] && echo YES || echo NO"

2. Schedule manual reboots during maintenance windows
3. Use PatchMon dashboard to track reboot requirements

Running patch scripts from an agent

Use your platform's command or terminal to run the patch scripts. Paths are relative to the skill directory (e.g.

_localsetup/skills/localsetup-linux-patcher/

or

_localsetup/skills/localsetup-linux-patcher/

); adjust for your layout.

• Automatic mode: Run

  scripts/patch-auto.sh

  (or

  scripts/patch-auto.sh --skip-docker

  for packages only). The script queries PatchMon for hosts needing updates, then runs package and optional Docker updates. Invoke via your platform's shell/exec/run capability.
• Scheduling: Use your platform's scheduler or system cron. Example (Linux cron):

  0 2 * * * cd /path/to/localsetup-linux-patcher && scripts/patch-auto.sh

  .
• Manual mode: For specific hosts, run

  scripts/patch-host-only.sh user@host

  or

  scripts/patch-host-full.sh user@host /path/to/docker/compose

  from your terminal or exec tool.
• Secrets: Store PatchMon credentials in your platform's secret store or in

  ~/.patchmon-credentials.conf

  ; see

  references/patchmon-setup.md

  .

What automatic mode does: Queries PatchMon for hosts needing updates, detects Docker on each host, updates system packages, and (unless

--skip-docker

) pulls Docker images and recreates containers. Docker updates are included by default; use

--skip-docker

to skip container updates.

Documentation Files

This skill includes comprehensive documentation:

• SKILL.md (this file) - Overview and usage guide
• SETUP.md - Complete setup instructions with security best practices
• WORKFLOWS.md - Visual workflow diagrams for all modes
• references/patchmon-setup.md - PatchMon installation and integration

First time setup? Read

SETUP.md

first - it provides step-by-step instructions for secure configuration.

Want to understand the flow? Check

WORKFLOWS.md

for visual diagrams of how the skill operates.

Supported Linux Distributions

Distribution	Package Manager	Tested	Status
Ubuntu	apt	[OK] Yes	Fully supported
Debian	apt	[WARNING] No	Supported (untested)
Amazon Linux 2	yum	[WARNING] No	Supported (untested)
Amazon Linux 2023	dnf	[WARNING] No	Supported (untested)
RHEL 7	yum	[WARNING] No	Supported (untested)
RHEL 8+	dnf	[WARNING] No	Supported (untested)
AlmaLinux	dnf	[WARNING] No	Supported (untested)
Rocky Linux	dnf	[WARNING] No	Supported (untested)
CentOS 7	yum	[WARNING] No	Supported (untested)
CentOS 8+	dnf	[WARNING] No	Supported (untested)
SUSE/OpenSUSE	zypper	[WARNING] No	Supported (untested)

The skill automatically detects the distribution and selects the appropriate package manager.