Installation¶

This guide walks you through the installation process for Anatalyst. ALL OF THIS IS WIP AND WILL NEED TO BE UPDATED

Installation Methods¶

Method 1: Using docker (Recommended)¶

# Pull the Docker image
docker pull ghcr.io/yourusername/downstream-scrnaseq:latest

Using devcontainer (For Development)¶

If you're using Visual Studio Code, a devcontainer configuration is provided in the .devcontainer folder. This allows you to develop within a container that has all dependencies pre-installed.

Install the Remote Development extension pack in VS Code
Open the repository folder in VS Code
When prompted, click "Reopen in Container"
VS Code will build the container and provide you with a fully configured development environment

Troubleshooting¶

Common Issues¶

R Bridge Connection Issues¶

If the R bridge fails to connect:

Error in R bridge: /bin/sh: 1: Rscript: not found

Make sure R is installed and the Rscript executable is in your PATH.

Memory Errors with Large Datasets¶

If you encounter memory errors when processing large datasets:

MemoryError: Unable to allocate array with shape...

Try increasing the memory limit in your configuration file:

pipeline:
  r_memory_limit_gb: 16  # Increase this value

For additional issues, please check the GitHub Issues (dead link for now) page or submit a new issue.