Installing slide_snake

slide_snake is a flexible Snakemake workflow for processing spatial RNA-sequencing data from various commercial and custom platforms. This guide will walk you through the installation process and initial setup.

Quick Installation

Step 1: Clone the Repository

git clone https://github.com/mckellardw/slide_snake.git
cd slide_snake

Step 2: Create Environment from Provided File

Install the base environment using the provided environment file:

mamba env create --file=envs/slsn.yml
mamba activate slsn

This will install all necessary dependencies including Snakemake, alignment tools, and analysis packages.

Step 3: Test Installation

Verify your installation by running a dry-run on the test data:

snakemake --use-conda --conda-frontend mamba -j 4

  • Note - the first run will take much longer as all of the rule-specific conda environments need to be built.

Post-Installation Setup

1. Configuration

Edit the main configuration file:

  • Update SAMPLE_SHEET_PATH to point to your actual sample sheet (default will point to the included toy datasets)

2. Reference Genomes

You’ll need to prepare STAR and/or kallisto references before running analyses. See the Reference Genomes documentation for detailed instructions.

3. Sample Sheet

Create your sample sheet following the format described in Sample Sheets.

Testing Your Installation

Run the pipeline on provided test data:

# Local run with 4 cores
snakemake -k -p --use-conda --conda-frontend mamba -j 4

# Test specific platform
snakemake out/test_sample/illumina/STAR/visium/counts_filtered/ -k -p --use-conda -j 4

Hardware Requirements

Minimum Requirements

  • CPU: 4 cores

  • RAM: 8GB

Common Installation Issues

Issue: Memory errors during alignment

Solution: Adjust memory limits in config.yaml:

MEMLIMIT_GB: 32G  # Adjust based on available RAM

Next Steps

  1. Read the Documentation: Start with Sample Sheets to understand input requirements

  2. Explore Recipes: Check Recipes to understand analysis options

  3. Prepare References: Follow Reference Genomes to set up your reference files

  4. Run Analysis: Choose between Short Read Pipeline or ONT Pipeline

Getting Help