setup_workspace.sh

#!/bin/bash
#
# Automatically sets up the working directory and structure

echo "====================================================="
echo "ECCFP Working Directory Setup Script"
echo "====================================================="

# Create the main working directory
echo "Creating eccfpws working directory..."
mkdir -p eccfpws

# Create the subdirectory structure
cd eccfpws
mkdir -p RawData Reference Software

echo "Directory structure created:"
echo " eccfpws/ - Main working directory"
echo " ├── RawData/ - Raw sequencing data"
echo " ├── Reference/ - Reference genome"
echo " └── Software/ - Software tools"

# Create symbolic links for example data (optional)
echo "Creating test data links..."
ln -sf ../test_data/fastq/SRR18143376_1k.fastq RawData/test_sample.fastq
ln -sf ../test_data/reference/GRCh38_chr21.fasta Reference/test_reference.fasta

echo "====================================================="
echo "Working directory setup complete!"
echo "Next steps:"
echo "1. Install software: cd scripts; bash install_all.sh"
echo "2. Run test: cd script; bash run_test.sh"
echo "====================================================="