go install github.com/nishad/srake/cmd/srake@latest

srake --version  # SRAKE - SRA Knowledge Engine

# Pull the image
docker pull ghcr.io/nishad/srake:latest

# Run with volume mounts for persistence
docker run -v ~/.local/share/srake:/data \
  -v ~/.cache/srake:/cache \
  ghcr.io/nishad/srake:latest \
  ingest --auto

# Linux/macOS
wget https://github.com/nishad/srake/releases/latest/download/srake-$(uname -s)-$(uname -m).tar.gz
tar -xzf srake-*.tar.gz
sudo mv srake /usr/local/bin/

srake --version

git clone https://github.com/nishad/srake.git
cd srake
go build -o srake ./cmd/srake
./srake --help

### Check Installation Verify srake is installed and check default paths: ```bash # Check version srake --version # View configured paths srake config paths ``` This will show where srake stores its data: - **Database**: `~/.local/share/srake/srake.db` - **Index**: `~/.cache/srake/index/srake.bleve` - **Downloads**: `~/.cache/srake/downloads/` - **Config**: `~/.config/srake/config.yaml` ### Ingest SRA Metadata Let srake automatically select and download the appropriate archive: ```bash srake ingest --auto ```Alternative ingestion methods:### Build Search Index Before searching, build the search index using the root-level `index` command: ```bash # Build initial index srake index --build # Build with progress display srake index --build --progress # Build with vector embeddings for semantic search srake index --build --with-embeddings # Verify index srake index --stats ``` ### Search Your Data **Simple Search**: ```bash srake search "homo sapiens" ``` **Quality-Controlled Search**: ```bash # Search with similarity threshold srake search "breast cancer" --similarity-threshold 0.7 --show-confidence # Return only top results srake search "RNA-Seq" --top-percentile 10 # Vector semantic search for related concepts srake search "tumor gene expression" --search-mode vector ``` **Filtered Search**: ```bash srake search "cancer" \ --organism "homo sapiens" \ --platform ILLUMINA \ --library-strategy RNA-Seq \ --limit 100 ``` **Search Modes**: ```bash # Database search (exact matching) srake search "SRP123456" --search-mode database # Full-text search (text matching) srake search "breast cancer" --search-mode fts # Hybrid search (best of both - default) srake search "RNA-Seq human" --search-mode hybrid # Vector search (semantic similarity) srake search "metabolic pathway analysis" --search-mode vector ``` **Export Results**: ```bash # JSON format srake search "RNA-Seq" --format json --output results.json # CSV with specific fields srake search "cancer" --format csv --fields "accession,organism,platform" # XML format srake search "transcriptome" --format xml --output results.xml ``` ### Convert Accessions Convert between SRA, GEO, and BioProject identifiers: ```bash # SRA to GEO srake convert SRP123456 --to GSE # GEO to SRA srake convert GSM123456 --to SRX # Batch conversion srake convert SRP001 SRP002 --to GSE --format json ``` ### Query Relationships Navigate the relationships between SRA entities: ```bash # Get all runs for a study srake runs SRP123456 # Get samples for an experiment srake samples SRX123456 --detailed # Get parent study from any accession srake studies SRR123456 ``` ### Download Data Download SRA files from multiple sources: ```bash # Basic download srake download SRR123456 # Download from AWS srake download SRR123456 --source aws --threads 4 # Download all runs for a study srake download SRP123456 --type fastq --parallel 4 ``` ### Start API Server Launch the REST API server with AI integration support: ```bash # Start server with all features srake server --port 8082 --enable-cors --enable-mcp # Custom configuration srake server --port 3000 --host 0.0.0.0 --enable-cors # With specific database and index SRAKE_DB_PATH=test.db SRAKE_INDEX_PATH=/tmp/index srake server ```### Manage Cache & Configuration Control disk usage and customize settings: ```bash # View cache usage srake cache info # Clean old downloads (free up space) srake cache clean --older 30d # Initialize configuration srake config init # Edit configuration srake config edit # Check all paths and environment variables srake config paths ```

# Use --yes flag to skip all prompts
srake ingest --auto --yes
srake download SRP123456 --yes

# Commands accept stdin for easy chaining
echo "SRP123456" | srake convert --to GSE
cat accessions.txt | srake download --parallel 4
srake search "RNA-Seq" | srake download --type fastq

# Preview actions without executing
srake download SRP123456 --dry-run

# Enable debug output for troubleshooting
srake convert SRP123456 --to GSE --debug

# Export in various formats for processing
srake search "human" --format json | jq '.results[].accession'
srake convert SRP123456 --to GSE --format csv > results.csv

# Human data only (taxonomy ID 9606)
srake ingest --file archive.tar.gz \
  --taxon-ids 9606

# Human, mouse, and zebrafish
srake ingest --file archive.tar.gz \
  --taxon-ids 9606,10090,7955

# Exclude viruses
srake ingest --file archive.tar.gz \
  --exclude-taxon-ids 32630,2697049

# Data from 2024 only
srake ingest --file archive.tar.gz \
  --date-from 2024-01-01 \
  --date-to 2024-12-31

srake ingest --file archive.tar.gz \
  --platforms ILLUMINA \
  --strategies RNA-Seq

srake ingest --file archive.tar.gz \
  --platforms OXFORD_NANOPORE \
  --strategies WGS

# High-quality data only
srake ingest --file archive.tar.gz \
  --min-reads 10000000 \
  --min-bases 1000000000

### Automatic Resume ```bash # If interrupted, run the same command again srake ingest --file archive.tar.gz # Output: # Previous ingestion found: # Progress: 45.3% complete # Resume? (y/n): y ``` ### Check Status ```bash srake ingest --status # Current Ingestion Status # ──────────────────────── # Progress: 67.8% complete # Records: 2,345,678 # ETA: 12 minutes ``` ### Force Restart ```bash # Start fresh (ignore existing progress) srake ingest --file archive.tar.gz --force ```

srake db info

# Shows:
# • Database size
# • Table counts
# • Index status

srake ingest \
  --file archive.tar.gz \
  --db /custom/path/db.sqlite

srake ingest \
  --file archive.tar.gz \
  --verbose

# Adjust checkpoint frequency
srake ingest --file archive.tar.gz \
  --checkpoint 5000

# Disable progress bar
srake ingest --file archive.tar.gz \
  --no-progress

# Set worker count
srake ingest --file archive.tar.gz \
  --workers 8