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
CondaTainer
Index
Edit on GitHub
Index