Open OnDemand

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### Starter Def File for VNC Container

Source: https://osc.github.io/ood-documentation/latest/reference/files/submit-yml/vnc-container-bc-options.html

An example Singularity definition file (.def) for creating a VNC container. It includes environment setup and package installations for XFCE, Python, websockify, and turbovnc.

```dockerfile
Bootstrap: docker

From: rockylinux/rockylinux:8

%environment
  PATH=/opt/TurboVNC/bin:$PATH
  LANGUAGE="en_US.UTF-8"
  LC_ALL="en_US.UTF-8"
  LANG="en_US.UTF-8"

%post
    dnf install -y epel-release
    dnf groupinstall -y xfce
    dnf install -y python3-pip xorg-x11-xauth
    pip3 install ts
    dnf install -y https://yum.osc.edu/ondemand/latest/compute/el8Server/x86_64/python3-websockify-0.10.0-1.el8.noarch.rpm
    dnf install -y https://yum.osc.edu/ondemand/latest/compute/el8Server/x86_64/turbovnc-2.2.5-1.el8.x86_64.rpm
    dnf clean all
    chown root:root /opt/TurboVNC/etc/turbovncserver-security.conf
    rm -rf /var/cache/dnf/*
```

--------------------------------

### Bash Scripting: Example Main Script (Simple HTTP Server)

Source: https://osc.github.io/ood-documentation/latest/how-tos/app-development/interactive/template.html

This `template/script.sh` example shows how to launch a simple HTTP web server using Python's `SimpleHTTPServer`. It first purges existing module environments, loads the Python module, and then starts the server on the dynamically assigned port. Authentication is not included in this basic example.

```bash
#!/bin/bash -l

# Purge the module environment to avoid conflicts with user-specified
# initialization files
module purge

# Load the Python module
module load python

# Launch the simple HTTP web server
python -m SimpleHTTPServer "${port}"

```

--------------------------------

### Container Start Arguments Configuration Example

Source: https://osc.github.io/ood-documentation/latest/reference/files/submit-yml/vnc-container-bc-options.html

Defines additional arguments to be passed to the container start command. This can be used to customize the container's execution environment.

```yaml
container_start_args: []
```

```yaml
container_start_args:
  - "--fakeroot"
```

--------------------------------

### Container Module Loading Configuration Example

Source: https://osc.github.io/ood-documentation/latest/reference/files/submit-yml/vnc-container-bc-options.html

Demonstrates how to specify the module to load before starting the container. This is useful for environments where specific software modules need to be activated.

```yaml
container_module: "singularity"
```

```yaml
container_module: "singularity/1.1.3"
```

--------------------------------

### Bash Scripting: Example Before Hook

Source: https://osc.github.io/ood-documentation/latest/how-tos/app-development/interactive/template.html

This example demonstrates a `template/before.sh` script that utilizes `find_port` to get an available port and `create_passwd` to generate a password. It exports these as environment variables and creates a password file, which are essential for securing web server access.

```bash
# Find available port to run web server on
export port=$(find_port)

# Define a password and password file used for authentication
password="$(create_passwd 12)"
export PASSWORD_FILE="${PWD}/passwd"

# Create password file used by web server
(umask 077 && echo "${password}" > "${PASSWORD_FILE}")

```

--------------------------------

### Install Python Packages with requirements.txt

Source: https://osc.github.io/ood-documentation/latest/tutorials/tutorials-passenger-apps/python-starter-app.html

This snippet details how to specify application dependencies in a `requirements.txt` file and then install them within an activated virtual environment using pip. It includes creating the `requirements.txt` file and the commands to activate the environment and install the packages.

```text
# requirements.txt
flask
```

```bash
source python-hello-world/bin/activate
python3 -m pip install -r requirements.txt
```

--------------------------------

### Start Keycloak Server using systemd

Source: https://osc.github.io/ood-documentation/latest/authentication/tutorial-oidc-keycloak-rhel7/install-keycloak.html

This snippet defines a systemd service file (`keycloak.service`) to manage the Keycloak server. It specifies the user, group, and the command to start the Keycloak standalone script. It also includes commands to reload the systemd daemon, start the Keycloak service, and check its status.

```bash
sudo cat > /etc/systemd/system/keycloak.service <<EOF

[Unit]
Description=Jboss Application Server
After=network.target

[Service]
Type=idle
User=keycloak
Group=keycloak
ExecStart=/opt/keycloak-9.0.0/bin/standalone.sh -b 0.0.0.0
TimeoutStartSec=600
TimeoutStopSec=600

[Install]
WantedBy=multi-user.target
EOF

sudo systemctl daemon-reload
sudo systemctl start keycloak
sudo systemctl status keycloak
```

--------------------------------

### Configure Init Containers for Pre-Application Setup

Source: https://osc.github.io/ood-documentation/latest/tutorials/tutorials-interactive-apps/k8s-jupyter.html

Shows how to define init containers that perform tasks before the main application starts. This example uses a utility image to save passwords as secrets and configure Jupyter notebook settings.

```yaml
init_containers:
- name: "init-secret"
  image: "<%= utility_img %>"
  command:
  - "/bin/save_passwd_as_secret"
  - "user-<%= user.name %>"
```

--------------------------------

### Enable and Start Dex Service

Source: https://osc.github.io/ood-documentation/latest/release-notes/v1.8-release-notes.html

Enables the `ondemand-dex` service to start automatically on boot and then starts the service immediately. This is required if the `ondemand-dex` package was installed and Dex authentication is being used.

```shell
sudo systemctl enable ondemand-dex.service
sudo systemctl start ondemand-dex.service
```

--------------------------------

### Install and Start ondemand_exporter via RPM

Source: https://osc.github.io/ood-documentation/latest/how-tos/monitoring/prometheus.html

Commands to install the exporter package on RHEL-based systems and initialize the service.

```bash
sudo yum install ondemand_exporter
sudo systemctl restart httpd
sudo systemctl start ondemand_exporter
```

--------------------------------

### Full submit.yml Example for Jupyter Notebook

Source: https://osc.github.io/ood-documentation/latest/tutorials/tutorials-interactive-apps/k8s-jupyter.html

A comprehensive example of a submit.yml file for launching a Jupyter notebook. It includes script configurations, container settings, environment variables, port mapping, resource allocation, configmap setup, host/NFS mounts, and multiple init containers for pre-launch configuration.

```yaml
# submit.yml.erb
<% 
 pwd_cfg = "c.NotebookApp.password=u'sha1:${SALT}:${PASSWORD_SHA1}'"
 host_port_cfg = "c.NotebookApp.base_url='/node/${HOST_CFG}/${PORT_CFG}/'"

 configmap_filename = "ondemand_config.py"
 configmap_data = "c.NotebookApp.port = 8080"
 utility_img = "docker.io/ohiosupercomputer/ood-k8s-utils:v1.0.0"

 user = OodSupport::User.new
%>
---
script:
accounting_id: "<%= account %>"
wall_time: "<%= wall_time.to_i * 3600 %>"
native:

  # here's the bulk of setting up the container. You'll likely need to specify all of these.
  container:
    name: "jupyter"
    image: "docker.io/jupyter/scipy-notebook:python-3.9.7"
    command: "/usr/local/bin/start.sh /opt/conda/bin/jupyter notebook --config=/ood/ondemand_config.py"
    working_dir: "<%= Etc.getpwnam(ENV['USER']).dir %>"
    restart_policy: 'OnFailure'
    env:
      NB_UID: "<%= user.uid %>"
      NB_USER: "<%= user.name %>"
      NB_GID: "<%= user.group.id %>"
      HOME: "<%= user.home %>"
    port: "8080"
    cpu: "<%= cpu %>"
    memory: "<%= memory %>Gi"
  configmap:
    files:
      - filename: "<%= configmap_filename %>"
        data: |
          c.NotebookApp.port = 8080
          c.NotebookApp.ip = '0.0.0.0'
          c.NotebookApp.disable_check_xsrf = True
          c.NotebookApp.allow_origin = '*'
          c.Application.log_level = 'DEBUG'
        mount_path: '/ood'
  mounts:
    - type: host
      name: home
      host_type: Directory
      path: <%= user.home %>
      destination_path: <%= user.home %>
  init_containers:
  - name: "init-secret"
    image: "<%= utility_img %>"
    command:
    - "/bin/save_passwd_as_secret"
    - "user-<%= user.name %>"
  - name: "add-passwd-to-cfg"
    image: "<%= utility_img %>"
    command:
    - "/bin/bash"
    - "-c"
    - "source /bin/passwd_from_secret; source /bin/create_salt_and_sha1; /bin/add_line_to_configmap \"<%= pwd_cfg %>\" <%= configmap_filename %>"
  - name: "add-hostport-to-cfg"
    image: "<%= utility_img %>"
    command:
    - "/bin/bash"
    - "-c"
    - "source /bin/find_host_port; /bin/add_line_to_configmap \"<%= host_port_cfg %>\" <%= configmap_filename %>"
```

--------------------------------

### Start and Enable libcgroup Services

Source: https://osc.github.io/ood-documentation/latest/installation/resource-manager/linuxhost.html

Commands to start and enable the `cgconfig` and `cgred` services, which are necessary for applying cgroup configurations and rules.

```bash
sudo systemctl start cgconfig
sudo systemctl start cgred
sudo systemctl enable cgconfig
sudo systemctl enable cgred

```

--------------------------------

### Manage Ruby Dependencies

Source: https://osc.github.io/ood-documentation/latest/tutorials/tutorials-passenger-apps/ruby-starter-app.html

Defines application dependencies using a Gemfile and installs them locally into the vendor/bundle directory.

```ruby
# frozen_string_literal: true

source 'https://rubygems.org'

gem 'sinatra'
```

```bash
bundle config path --local vendor/bundle
bundle install
```

--------------------------------

### Initialize cleanup environment

Source: https://osc.github.io/ood-documentation/latest/reference/files/submit-yml/basic-bc-options.html

Example of setting the PATH and sourcing the cleanup script in a shell environment.

```Bash
PATH=$PATH:/opt/ood-clean/bin source clean.sh
```

--------------------------------

### Start Listening Server with Netcat (Bash)

Source: https://osc.github.io/ood-documentation/latest/how-tos/app-development/interactive/setup/enable-reverse-proxy.html

This bash command uses netcat (nc) to start a simple listening server on a specified port (5432 in this example). This is used to test the reverse proxy by allowing connections from the browser to a service running on a compute node.

```bash
nc -l 5432

```

--------------------------------

### Install ondemand_exporter from Source

Source: https://osc.github.io/ood-documentation/latest/how-tos/monitoring/prometheus.html

Manual installation steps for downloading, extracting, and configuring the exporter binary and systemd service.

```bash
VERSION="0.10.0"
ARCHIVE="ondemand_exporter-${VERSION}.linux-amd64"
wget -O /tmp/${ARCHIVE}.tar.gz https://github.com/OSC/ondemand_exporter/releases/download/v${VERSION}/${ARCHIVE}.tar.gz
tar xf /tmp/${ARCHIVE}.tar.gz -C /tmp
sudo install -o root -g root -m 0755 /tmp/${ARCHIVE}/ondemand_exporter /usr/bin/ondemand_exporter
sudo install -o root -g root -m 0440 /tmp/${ARCHIVE}/files/sudo /etc/sudoers.d/ondemand_exporter
sudo install -o root -g root -m 0644 /tmp/${ARCHIVE}/files/ondemand_exporter.service /etc/systemd/system/
sudo systemctl daemon-reload
```

--------------------------------

### Build and install Dex from source

Source: https://osc.github.io/ood-documentation/latest/authentication/dex.html

Compiles the Dex binary from the official repository, sets up the required system user/group, and installs necessary web assets and systemd service files.

```bash
GOPATH=$(go env GOPATH)
go get github.com/dexidp/dex
cd $GOPATH/src/github.com/dexidp/dex
make build
sudo install -m 0755 bin/dex /usr/sbin/ondemand-dex

sudo groupadd -r ondemand-dex
sudo useradd -r -d /var/lib/ondemand-dex -g ondemand-dex -s /sbin/nologin -c "OnDemand Dex" ondemand-dex

cd /tmp
git clone https://github.com/OSC/ondemand-dex
sudo mkdir /usr/share/ondemand-dex
sudo cp -R ondemand-dex/web /usr/share/ondemand-dex/web
sudo install -m 0644 ondemand-dex/examples/ondemand-dex.service /etc/systemd/system/ondemand-dex.service
```

--------------------------------

### Download and Unpack Keycloak

Source: https://osc.github.io/ood-documentation/latest/authentication/tutorial-oidc-keycloak-rhel7/install-keycloak.html

Downloads Keycloak 9.0.0 and unpacks it to the /opt directory. This is the initial step for setting up the Keycloak server.

```bash
cd /opt
sudo wget https://downloads.jboss.org/keycloak/9.0.0/keycloak-9.0.0.tar.gz
sudo tar xzf keycloak-9.0.0.tar.gz
```

--------------------------------

### Install Dex Authentication Package

Source: https://osc.github.io/ood-documentation/latest/release-notes/v1.8-release-notes.html

Installs the `ondemand-dex` package, which is recommended for sites previously using Apache's Basic Auth (e.g., with LDAP) to switch to Dex Authentication. This package provides the Dex OIDC provider for OnDemand.

```shell
sudo yum install ondemand-dex
```

--------------------------------

### Download and Install Kubectl on OnDemand Web Node

Source: https://osc.github.io/ood-documentation/latest/installation/resource-manager/kubernetes.html

Downloads and installs the kubectl binary on the OnDemand web node. This allows the web node to communicate with the Kubernetes cluster. Replace $VERSION with the desired Kubernetes version.

```bash
wget -O /usr/local/bin/kubectl https://storage.googleapis.com/kubernetes-release/release/v$VERSION/bin/linux/amd64/kubectl
chmod +x /usr/local/bin/kubectl

```

--------------------------------

### Dex Frontend Configuration Example

Source: https://osc.github.io/ood-documentation/latest/authentication/dex.html

Example of configuring the frontend theme and directory for Dex. This setting affects the look and feel of the Dex interface. The 'dir' key specifies the web assets directory, and 'theme' sets the visual theme.

```yaml
frontend:
  dir: "/usr/share/ondemand-dex/web"
  theme: "ondemand"
```

--------------------------------

### Install JDK 1.8.0

Source: https://osc.github.io/ood-documentation/latest/authentication/tutorial-oidc-keycloak-rhel7/install-keycloak.html

Installs the OpenJDK 1.8.0 development kit, which is a prerequisite for running Keycloak.

```bash
sudo yum install java-1.8.0-openjdk-devel
```

--------------------------------

### Basic submit.yml.erb Example

Source: https://osc.github.io/ood-documentation/latest/reference/files/submit-yml-erb.html

A simple example of a submit.yml.erb file demonstrating the 'script' and 'batch_connect' attributes with a 'basic' template.

```erb
# a simple script.yml.erb file

script:
  native:
    - "-n"
    - "1"
batch_connect:
  template: "basic"
  header: "#!/bin/bash"
```

--------------------------------

### Create Keycloak User and Set Ownership

Source: https://osc.github.io/ood-documentation/latest/authentication/tutorial-oidc-keycloak-rhel7/install-keycloak.html

Creates a dedicated 'keycloak' user and group, and sets the ownership of the Keycloak installation directory to this user. This ensures proper permissions for running the Keycloak server.

```bash
sudo groupadd -r keycloak
sudo useradd -m -d /var/lib/keycloak -s /sbin/nologin -r -g keycloak keycloak
sudo install -d -o keycloak -g keycloak /var/lib/keycloak
sudo chown keycloak: -R keycloak-9.0.0
```

--------------------------------

### Pass Native Scheduler Arguments (SLURM Example)

Source: https://osc.github.io/ood-documentation/latest/reference/files/submit-yml/script.html

Allows passing native arguments directly to the scheduler's submit command. This example demonstrates SLURM-specific arguments for nodes, cores, and memory, using form variables.

```yaml
native:
  - "-N"
  - "1"
  - "-n"
  - "<%= num_cores %>"
  - "--mem"
  - "<%= memory %>"
```

--------------------------------

### Install and Build Keycloak Duo SPI

Source: https://osc.github.io/ood-documentation/latest/authentication/duo-2fa-with-keycloak.html

Commands to clone the repository, build the SPI using either Docker or local Maven, and deploy the resulting JAR and template files to the Keycloak installation directory.

```bash
git clone https://github.com/OSC/keycloak-duo-spi.git
cd keycloak-duo-spi
git submodule update --init
```

```bash
docker run --rm -it -v $(pwd):/keycloak-duo-spi -w /keycloak-duo-spi \
  ohiosupercomputer/keycloak_duo_spi_buildbox:latest mvn clean test package
```

```bash
yum -y install maven
cd build/duo_java/DuoWeb
mvn clean test install
cd ../../..
mvn clean test package
```

```bash
sudo install -o keycloak -g keycloak -m 0644 target/keycloak-duo-spi-jar-with-dependencies.jar \
  /opt/keycloak-9.0.0/standalone/deployments/keycloak-duo-spi-jar-with-dependencies.jar
sudo install -o keycloak -g keycloak -m 0644 src/main/resources/duo-mfa.ftl \
  /opt/keycloak-9.0.0/themes/base/login/duo-mfa.ftl
sudo install -o keycloak -g keycloak -m 0644 /dev/null \
  /opt/keycloak-9.0.0/standalone/deployments/keycloak-duo-spi-jar-with-dependencies.jar.dodeploy
```

--------------------------------

### Job Template Manifest Example

Source: https://osc.github.io/ood-documentation/latest/customizations.html

Defines the structure and example content for a job template's manifest.yml file, which includes metadata like name, host, script, and notes.

```yaml
name: A Template Name
host: ruby
script: ruby.sh
notes: Notes about the template, such as content and function.

```

--------------------------------

### Slurm bin_overrides Example (YAML)

Source: https://osc.github.io/ood-documentation/latest/installation/cluster-config-schema.html

This example demonstrates how to use 'bin_overrides' for the Slurm adapter to specify alternative paths for resource manager client executables. It shows overriding commands like squeue and sbatch, while noting that unsupported commands (like bsub for Slurm) are ignored.

```yaml
# An example in Slurm
job:
  adapter: "slurm"
  bin: "/opt/slurm/bin"
  conf: "/opt/slurm/etc/slurm.conf"
  bin_overrides:
      squeue: "/usr/local/slurm/bin/squeue_wrapper"
      # Override just want you want/need to
      # scontrol: "/usr/local/slurm/bin/scontrol_wrapper"
      sbatch: "/usr/local/slurm/bin/sbatch_wrapper"
      # Will be ignored because bsub is not a command used in the Slurm adapter
      bsub: "/opt/lsf/bin/bsub"

```

--------------------------------

### Cloudy Cluster YAML Configuration Example

Source: https://osc.github.io/ood-documentation/latest/installation/resource-manager/ccq.html

A sample YAML configuration file for setting up a Cloudy Cluster resource manager. This configuration specifies cluster metadata, login host, job adapter details, cloud provider, scheduler name, binary paths, and a regular expression for job ID extraction. It also includes commented-out examples for overriding CCQ client binaries.

```yaml
---
v2:
  metadata:
    title: "My Cluster"
  login:
    host: "my_cluster.my_center.edu"
  job:
    adapter: "ccq"
    image: "my-default-image"
    cloud: "gcp"
    scheduler: "my_scheduler"
    bin: "/path/to/other/CCQ"
    jobid_regex: "different job_id regex: (?<job_id>\\d+) "
    # bin_overrides:
      # ccqstat: "/usr/local/bin/ccqstat"
      # ccqdel: ""
      # ccqsub: ""

```

--------------------------------

### Update OnDemand Release RPM

Source: https://osc.github.io/ood-documentation/latest/release-notes/v1.8-release-notes.html

Installs the OnDemand release RPM for version 1.8, which is a prerequisite for updating OnDemand itself. This command uses `yum` to install the specified RPM package from a URL.

```shell
sudo yum install -y https://yum.osc.edu/ondemand/1.8/ondemand-release-web-1.8-1.noarch.rpm
```

--------------------------------

### Configure config.ru for Ruby Applications

Source: https://osc.github.io/ood-documentation/latest/tutorials/tutorials-passenger-apps/ruby-starter-app.html

Defines the entry point for Rack-based Ruby applications. Includes specific configurations for Sinatra and Ruby on Rails frameworks.

```ruby
# frozen_string_literal: true

require_relative 'app'
run App
```

```ruby
# frozen_string_literal: true

require_relative 'config/environment'

run Rails.application
Rails.application.load_server
```

--------------------------------

### Create Basic Python WSGI App Entrypoint

Source: https://osc.github.io/ood-documentation/latest/tutorials/tutorials-passenger-apps/python-starter-app.html

This snippet demonstrates creating the `passenger_wsgi.py` file, which serves as the entrypoint for a Python WSGI application. It outlines the necessary commands to create the file and provides the basic Python code to return a 'Hello World' message and the Python version.

```bash
cd ~/ondemand/dev
mkdir python-hello-world
cd python-hello-world
touch passenger_wsgi.py
```

```python
# passenger_wsgi.py
import sys

def application(environ, start_response):
    start_response('200 OK', [('Content-type', 'text/plain')])
    return ["Hello World from Open OnDemand (Python WSGI)!\n\n" + sys.version]
```

--------------------------------

### Update OnDemand Release RPM (Bash)

Source: https://osc.github.io/ood-documentation/latest/release-notes/v1.7-release-notes.html

Installs the OnDemand release RPM for version 1.7. This is the first step in the upgrade process.

```bash
sudo yum install -y https://yum.osc.edu/ondemand/1.7/ondemand-release-web-1.7-1.noarch.rpm

```

--------------------------------

### Configure and Deploy Application Manifest

Source: https://osc.github.io/ood-documentation/latest/tutorials/tutorials-passenger-apps/ruby-starter-app.html

Configures the manifest.yml for dashboard integration and provides shell commands for version control and production deployment.

```yaml
name: Quota
description: Display quotas
icon: fa://hdd-o
category: Files
subcategory: Utilities
```

```bash
git add .
git commit -m "update manifest for production"
git push origin master

# as sudo on OnDemand host:
cd /var/www/ood/apps/sys
git clone /users/PZS0562/efranz/ondemand/dev/quota
```

--------------------------------

### Define Application Configuration and Paths

Source: https://osc.github.io/ood-documentation/latest/reference/files/nginx-stage-yml.html

Configures how Open OnDemand discovers and serves applications. Includes definitions for app configuration files, root directories, and request URI patterns.

```yaml
pun_app_configs:
  - env: dev
    name: "*"
    owner: "%{user}"

app_config_path:
  dev: "/var/lib/ondemand-nginx/config/apps/dev/%{owner}/%{name}.conf"
  usr: "/var/lib/ondemand-nginx/config/apps/usr/%{owner}/%{name}.conf"
  sys: "/var/lib/ondemand-nginx/config/apps/sys/%{name}.conf"

app_root:
  dev: "/var/www/ood/apps/dev/%{owner}/gateway/%{name}"
  usr: "/var/www/ood/apps/usr/%{owner}/gateway/%{name}"
  sys: "/var/www/ood/apps/sys/%{name}"

app_request_uri:
  dev: "/dev/%{name}"
  usr: "/usr/%{owner}/%{name}"
  sys: "/sys/%{name}"
```

--------------------------------

### Include Sinatra Gems in Gemfile

Source: https://osc.github.io/ood-documentation/latest/release-notes/v1.8-release-notes.html

Adds essential Sinatra gems to the application Gemfile, allowing lightweight Ruby applications to run without local dependency installation.

```ruby
gem "sinatra", require: false
gem "sinatra-contrib", require: false
gem "erubi", require: false
```

--------------------------------

### Update OnDemand Package

Source: https://osc.github.io/ood-documentation/latest/release-notes/v1.8-release-notes.html

Cleans the yum cache and then updates the OnDemand package to the latest available version. This ensures that all OnDemand components are brought up to date after the release RPM has been installed.

```shell
sudo yum clean all
sudo yum update ondemand
```

--------------------------------

### Implement Sinatra Application Logic

Source: https://osc.github.io/ood-documentation/latest/tutorials/tutorials-passenger-apps/ruby-starter-app.html

A basic implementation of a Sinatra application class that defines a root route returning 'Hello World'.

```ruby
require 'sinatra/base'

class App < Sinatra::Base
  get '/' do
    'Hello World'
  end
end
```

--------------------------------

### Container Command Configuration Example

Source: https://osc.github.io/ood-documentation/latest/reference/files/submit-yml/vnc-container-bc-options.html

Specifies the command used to initiate the container. This allows flexibility in choosing the container runtime, such as 'singularity' or 'apptainer'.

```yaml
container_module: "singularity"
```

```yaml
container_module: "apptainer"
```

--------------------------------

### Add Help Text to Form Field

Source: https://osc.github.io/ood-documentation/latest/how-tos/app-development/interactive/form.html

This snippet shows how to add descriptive help text below a form field. The 'help' option supports Markdown formatting, allowing for rich text explanations, bullet points, and code examples to guide the user.

```yaml
help: |
  Please fill in this field with **one** of the following
  options:

  - `red`
  - `blue`
  - `green`

```

--------------------------------

### Copy Application to Production Directory

Source: https://osc.github.io/ood-documentation/latest/tutorials/tutorials-passenger-apps/nodejs-starter-app.html

This command, executed as root (sudo) on the OnDemand host, clones a user's development application repository into the system's production applications directory (`/var/www/ood/apps/sys`). This is the final step in making the application available in the production environment.

```bash
# as sudo on OnDemand host:
cd /var/www/ood/apps/sys
git clone /users/PZS0562/efranz/ondemand/dev/quota
```

--------------------------------

### Custom Error Page for Missing Home Directory

Source: https://osc.github.io/ood-documentation/latest/customizations.html

Provides an example of a custom HTML error page to display when a user's home directory is missing upon launching an OnDemand application. This page guides the user to create their home directory using the shell app.

```html
<!DOCTYPE html>
<html>
<head>
  <title>Home Directory Missing</title>
</head>
<body>
  <h1>Your home directory is missing.</h1>
  <p>Please click the link below to open a shell and create your home directory.</p>
  <a href="/pun/dev/shell/">Open Shell</a>
</body>
</html>

```

--------------------------------

### Create Custom Ruby Wrapper

Source: https://osc.github.io/ood-documentation/latest/tutorials/tutorials-passenger-apps/ruby-starter-app.html

A shell script wrapper to execute the application using a specific version of Ruby, overriding the default environment.

```bash
#!/bin/bash

# OnDemand uses ruby 3.3, but this application uses 3.0.

module load ruby/3.0
exec /bin/env ruby "$@"
```

--------------------------------

### Set OOD Cluster Attribute Values (num_cores)

Source: https://osc.github.io/ood-documentation/latest/tutorials/tutorials-interactive-apps/add-matlab/edit-form-yml.html

Specifies attribute values for form elements within an Open OnDemand cluster configuration. This example shows how to set minimum, maximum, and step values for the 'num_cores' attribute, tailored for the OSC Owens cluster. It also includes a help text to guide the user.

```yaml
---
attributes:
  num_cores:
    widget: "number_field"
    label: "Number of cores"
    value: 1
    help: |
      Number of cores on node type (4 GB per core unless requesting whole
      node). Leave blank if requesting full node.
    min: 0
    max: 48
    step: 1
    id: 'num_cores'

```

--------------------------------

### Install OnDemand Release RPM (Bash)

Source: https://osc.github.io/ood-documentation/latest/release-notes/v2.0-release-notes.html

Command to install the OnDemand release RPM package, which is the first step in upgrading OnDemand. This command uses `yum` to install from a provided URL.

```bash
sudo yum install -y https://yum.osc.edu/ondemand/2.0/ondemand-release-web-2.0-1.noarch.rpm
```

--------------------------------

### Configure Interactive App for Singularity Container

Source: https://osc.github.io/ood-documentation/latest/installation/resource-manager/linuxhost.html

Example configuration for a submit.yml file to define Singularity bind paths and container images for an interactive application.

```yaml
---
batch_connect:
  template: vnc
script:
  native:
     singularity_bindpath: /fs,/home
     singularity_container: /usr/local/modules/netbeans/netbeans_2019.sif
```

--------------------------------

### Install ondemand-dex package

Source: https://osc.github.io/ood-documentation/latest/authentication/dex.html

Installs the Dex authentication package using system package managers for RHEL/CentOS or Debian/Ubuntu distributions.

```bash
sudo yum install ondemand-dex
```

```bash
sudo apt-get install ondemand-dex
```

--------------------------------

### Initialize Node.js Application

Source: https://osc.github.io/ood-documentation/latest/tutorials/tutorials-passenger-apps/nodejs-starter-app.html

Initializes a new Node.js application directory and its package.json file using npm. It's important to note that for OnDemand to recognize the application, the 'main' attribute in package.json should be 'app.js', not the default 'index.js'.

```bash
cd ~/ondemand/dev
mkdir nodejs-hello-world
cd nodejs-hello-world
npm init
```

--------------------------------

### Restrict Access to Keycloak Standalone Directory

Source: https://osc.github.io/ood-documentation/latest/authentication/tutorial-oidc-keycloak-rhel7/install-keycloak.html

Restricts access to the 'standalone' directory within the Keycloak installation to the 'keycloak' user. This is a security measure to protect sensitive server data.

```bash
cd keycloak-9.0.0
sudo -u keycloak chmod 700 standalone
```

--------------------------------

### Add Express Web Framework to Node.js App

Source: https://osc.github.io/ood-documentation/latest/tutorials/tutorials-passenger-apps/nodejs-starter-app.html

Adds the Express web framework to a Node.js project and installs the necessary packages. Express is used to route requests to appropriate pages within the application.

```bash
npm add express
npm install
```

--------------------------------

### Define Job Start Time

Source: https://osc.github.io/ood-documentation/latest/reference/files/submit-yml/script.html

Specifies the desired start time for the job. If not set (nil), schedulers typically interpret it as 'now' or 'as soon as possible'.

```yaml
start_time: nil
```

```yaml
start_time: "00:00:00"
```

--------------------------------

### Display nginx_stage Help Reference

Source: https://osc.github.io/ood-documentation/latest/reference/commands/nginx-stage/usage.html

This command displays a quick reference of the capabilities offered by the nginx_stage utility. It is useful for understanding the available commands and their general options.

```bash
nginx_stage [COMMAND] --help

```

--------------------------------

### Container Bind Path Configuration Example

Source: https://osc.github.io/ood-documentation/latest/reference/files/submit-yml/vnc-container-bc-options.html

Shows how to configure paths to be mounted inside the container. This allows access to host file systems or specific directories from within the containerized VNC session.

```yaml
container_bindpath: ""
```

```yaml
container_bindpath: "/etc,/dev,/usr"
```

--------------------------------

### Scan MapFile using ood_auth_map utility

Source: https://osc.github.io/ood-documentation/latest/authentication/overview/map-user.html

Demonstrates how to use the ood_auth_map binary to resolve remote usernames to local users. It covers both default and custom mapfile locations, as well as the behavior when no mapping is found.

```bash
# Scan default mapfile with URL-encoded username
/opt/ood/ood_auth_map/bin/ood_auth_map.mapfile 'http%3A%2F%2Fcilogon.org%2FserverA%2Fusers%2F58606%40cilogon.org'

# Scan custom mapfile with standard username
/opt/ood/ood_auth_map/bin/ood_auth_map.mapfile --file '/path/to/mapfile' 'opaque_remote_username'

# Example of no match found
/opt/ood/ood_auth_map/bin/ood_auth_map.mapfile 'this_remote_username_does_not_exist'
```

--------------------------------

### Install mod_auth_mellon for Apache

Source: https://osc.github.io/ood-documentation/latest/authentication/adfs-with-auth-mellon.html

Installs the mod_auth_mellon and mod_ssl modules for Apache HTTP Server on EL7, EL8, and Ubuntu systems. Ensure Software Collections are enabled for EL7/EL8.

```bash
yum install httpd24-mod_auth_mellon httpd24-mod_ssl
```

```bash
yum install mod_auth_mellon mod_ssl
```

```bash
apt install libapache2-mod-auth-mellon
```

--------------------------------

### Install EPEL Release (Bash - CentOS/RHEL 7)

Source: https://osc.github.io/ood-documentation/latest/release-notes/v2.0-release-notes.html

Command to install the Extra Packages for Enterprise Linux (EPEL) repository on CentOS/RHEL 7 systems, which provides additional packages not found in the base repositories.

```bash
sudo yum install epel-release
```

--------------------------------

### Create Python Virtual Environment Wrapper Script

Source: https://osc.github.io/ood-documentation/latest/tutorials/tutorials-passenger-apps/python-starter-app.html

This bash script acts as a wrapper to activate a Python virtual environment before executing a Python script. It determines the script's directory, sources the virtual environment's activation script, and then uses `exec` to run the Python interpreter with the provided arguments, ensuring dependencies are available.

```bash
#!/usr/bin/env bash

SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
source $SCRIPT_DIR/../python-hello-world/bin/activate

exec /bin/env python3 "$@"
```

--------------------------------

### Python Flask App with WSGI Entrypoint

Source: https://osc.github.io/ood-documentation/latest/tutorials/tutorials-passenger-apps/python-starter-app.html

This code demonstrates a more advanced Python application structure using Flask. It separates the application logic into `app.py` and uses `passenger_wsgi.py` to import and expose the Flask application as the WSGI entrypoint. This allows for better organization and dependency management.

```python
# passenger_wsgi.py
from app import MyApp as application
```

```python
# app.py
from flask import Flask
import sys

MyApp = Flask('python_hello_world')

@MyApp.route("/")
def index():
  return 'Hello World!<br>' + sys.version

if __name__ == "__main__":
  MyApp.run()
```

--------------------------------

### File User Mapping Script Usage

Source: https://osc.github.io/ood-documentation/latest/authentication/overview/map-user.html

Illustrates the command-line usage for the file-based user mapping script. It shows how to specify a mapfile and pass the REMOTE_USER for lookup.

```bash
/opt/ood/ood_auth_map/bin/ood_auth_map.mapfile -f /path/to/your/mapfile "authenticated_username"
```
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