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User Guide:

  • Installation
    • 📋 Prerequisites
    • 🛠️ Quick Installation
    • ✅ Verify Installation
    • ⚙️ Initialize Configuration
    • ⌨️ Shell Completion
    • 🗺️ Next Steps
    • 🗑️ Uninstallation
  • Concepts: Overlays
    • 💡 The Main Idea
    • 📦 Overlay Types
      • 🖥️ OS Overlays
      • 🧩 Module Overlays
      • 📂 Naming Convention
        • Version Delimiters
    • 🧱 Stacking Overlays
      • Stacking Example: Override cutadapt version in trim-galore
    • 🐍 Leveraging Conda Resources
    • 🔄 Module Workflow
  • Module Overlays
    • 👀 Quick Look
    • 📥 Installing Module Overlays
      • Normal Build Script Module
      • Template Script Module
    • 🚀 Dependencies Automation
      • 🧬 Data Overlay Installation
      • 🏷️ Declaring Dependencies in Scripts
    • 🤖 Scheduler Automation
    • 🧫 Case Study: Cellranger Count
      • 📜 Count Script
      • 📥 Install required overlays
      • 📤 Load and use overlays
    • 🔗 Related Resources
  • Writable Workspace Overlays
    • Table of Contents
    • Create a Workspace Overlay
      • Change the Overlay Size
    • Launch a Shell within the Workspace Overlay
    • Writable or Read-Only
    • Set Environment Variables for the Overlay
    • Use Workspace Overlay in a Script
    • Export the Conda Environment
    • Share the Overlay with Others
      • Permissions inside the overlay
    • Common Issues
      • Read-only file system
      • No space left on device
      • Permission errors when executing commands
      • The overlay is used by another process
  • Read-Only Bundle Overlays
    • Table of Contents
    • Create a Bundle Overlay
    • Launch a Shell within the Bundle Overlay
    • Use Bundle Overlays in a Script

Helpers:

  • Helper Scripts
    • How It Works
    • Prerequisites
      • Install CondaTainer
      • Download Helper Scripts
      • SSH Port Forwarding
      • HPC Scheduler
      • Clusters Without Inter-Node SSH
    • Quick Start
    • Flags
      • Resource Flags
      • Overlay Flags
      • Helper-Specific Flags
    • Configuration
      • Session History
      • Settings Confirmation
    • Available Applications
  • RStudio Server
    • rstudio-server (Posit R)
      • Writable Overlay
      • Flags
      • Installing R Packages
        • Rprofile Setup
        • Missing System Libraries
      • Run R Without RStudio
    • rstudio-server-conda (Conda R)
      • Writable Overlay with R
      • Package Management
      • Run R Without RStudio
    • Common Issues
      • UID conflict (UID = 1000)
  • VS Code
    • code-server
      • Flags
    • vscode-server
      • Flags
    • vscode-tunnel
      • Flags
      • Authentication
    • Common Issues
      • Inode quota issues
      • Connection token issues (vscode-server)
      • Machine name already taken (vscode-tunnel)
  • XFCE4 Desktop
    • VNC Provider
      • TurboVNC
      • KasmVNC
    • GPU
      • With KasmVNC (--vnc kasm)
      • With TurboVNC (--vnc turbo)
    • Flags
    • IGV
    • Cytoscape
      • Java version
      • CytoscapeConfiguration
    • Desktop Home Directory
    • Common Issues
      • Screen resolution
      • Audio not working (KasmVNC)

FAQ:

  • Exec Troubleshooting
    • If an overlay image cannot be mounted
      • Used by another process
        • On a Headless Server
        • On an HPC Cluster
        • After killing
      • Permission Denied Errors
        • Level 1: The Image File (Host)
        • Level 2: Inside the Overlay (Container)
    • If cannot write to an overlay image
      • Read-only File System
      • Overlay is Full
      • Permission Denied Errors in Container
  • OverlayFS and Fakeroot
    • OverlayFS
    • Fakeroot
      • Build the image with fakeroot
      • Run the container/overlay with fakeroot
    • How to Use
      • Installing missing system libraries
      • Changing Overlay Ownership
  • Scheduler Resources
    • Table of Contents
    • Concepts
      • Single-Task vs Multi-Task (MPI) Jobs
      • HTCondor: Single-Task Only
      • Array Jobs
      • Job Chaining
      • Array Jobs + Chaining
    • How Schedulers Define Resources
      • GPU support
    • How CondaTainer Handles Directives
      • Normalizing Directives and Passthrough Mode
      • Cross-Scheduler Translation
      • MPI Auto-Detection
    • Manual Submission

Manuals:

  • Build Script Manual
    • Table of Contents
    • Naming Conventions
      • OS
      • Apps
      • Data
      • Example
    • Available Variables
    • Headers
      • WhatIs and URL
      • Set Dependencies
      • Scheduler Parameters
      • Type Tag
      • Template Tags
      • Auto-Update Tag
      • Environment Variables
        • ENV Naming Guidelines
      • Interactive Tag
    • Apps
      • Tips
      • Examples
    • Data
      • Tips
      • Examples
  • CondaTainer Manual
    • Table of Contents
    • Overall Command Structure
    • Naming Convention
      • System Applications (OS)
      • Custom Environments (Bundle/Workspace)
      • Application Overlays (Module)
      • Reference Overlays (Module)
      • Rename or not to Rename?
    • Mount Points
    • Overlay
      • Overlay Create
      • Overlay Info
      • Overlay Check
      • Overlay Chown
      • Overlay Resize
      • Overlay Export
    • Create
      • System level Examples
      • Project level Examples
      • Exit Codes (script and job-submission behavior) ⚠️
    • Container Management (Avail, List, Remove, Search)
      • Avail
      • List
      • Remove
      • Search
    • Exec
    • E (Quick Exec)
      • Autoload and Shell Completion
    • Instance
      • Instance Start
      • Instance Stop
      • Instance List
      • Instance Stats
      • Instance Exec
      • Instance Workflow Example
    • Runtime (Check, Run)
      • Check
      • Run
      • Scheduler Integration
      • Script Arguments
      • Array Jobs
      • Job Chaining
      • Array Jobs + Chaining
      • Usable ENV
      • MPI Auto-Detection
      • CondaTainer is compatible with module systems
    • Info
      • SquashFS (.sqf) output
      • ext3 (.img) output
    • Helper
    • Config
      • Config Show
      • Config Get
      • Config Set
      • Config Append / Prepend / Remove
      • Config Init
      • Config Paths
      • Config Validate
      • Configuration Priority
      • Configuration File Example
    • Scheduler
    • Update
    • Self-Update
    • Proxy
      • Two modes
      • proxy start
      • proxy stop / status / show
      • Automatic injection (inside jobs)
      • proxy_perjob config option
    • Completion
  • Configuration
    • Configuration Priority
      • Environment Variables (admin override)
      • Config Files (layered)
    • Quick Start
    • Config File Locations
    • Configuration Options
      • Directories
      • Binaries
      • Remote Sources
      • Options
      • Build Configuration
    • Managing Configuration
      • View Configuration
      • Set Configuration Values
      • Manage Array Config Values
      • Validate Configuration
    • Environment Variables
    • Data Directory Search Paths
      • Search Priority
      • View Search Paths
      • Directory Structure
    • Example Config File
    • Time Duration Format
    • Standalone Installations
    • Multi-Tier Setup (System → Group → User)
    • Compression Settings
    • Block Size Settings
    • Troubleshooting
      • Config file not found
      • Apptainer/Singularity not found
      • Scheduler not detected
      • Scheduler commands timing out
      • Remote metadata unavailable or stale
      • Using multiple remote script sources
      • Disable job submission
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