BioContainers Registry

BioLang provides native access to the BioContainers registry — over 9,000 containerized bioinformatics tools with versioned Docker and Singularity images. Search, browse, and inspect tools directly from BioLang with built-in functions. No import needed.

Searching Tools

Use biocontainers_search() to find tools by name or keyword. Results include the tool name, description, organization, version count, and the latest image URI:

# Search for samtools
let results = biocontainers_search("samtools")
results |> print()
# => [{ name: "samtools", description: "...", organization: "biocontainers",
#        version_count: 42, latest_version: "1.19", latest_image: "quay.io/..." }, ...]

# Search with a result limit
biocontainers_search("bwa", 5) |> print()

# Search for alignment tools
biocontainers_search("alignment") |> print()

Returns a List of Records: {name, description, organization, version_count, latest_version, latest_image}. Default limit is 25.

Popular Tools

Browse the most popular tools in the registry with biocontainers_popular():

# Get top 20 most popular tools (default)
let popular = biocontainers_popular()
popular |> print()

# Get top 50
biocontainers_popular(50)
  |> map(|t| { name: t.name, versions: t.version_count })
  |> print()

Returns a List of Records with the same fields as biocontainers_search. Default limit is 20.

Tool Details

Get detailed metadata for a specific tool with biocontainers_info(), including all available versions and container images:

# Get full details for samtools
let info = biocontainers_info("samtools")
print(info)

# Access nested version data
print("Latest version:", info.latest_version)
print("Total versions:", info.version_count)

# List all available images for the latest version
info.versions
  |> first()
  |> get("images")
  |> print()

Returns a Record with nested versions and images.

Version Management

List all versions and their container image URIs for a tool with biocontainers_versions():

# List all versions of gatk4
let versions = biocontainers_versions("gatk4")
versions |> print()
# => [{ version: "4.5.0.0", images: ["quay.io/biocontainers/gatk4:4.5.0.0--...", ...] },
#     { version: "4.4.0.0", images: ["quay.io/biocontainers/gatk4:4.4.0.0--...", ...] },
#     ...]

# Get the latest version image
let latest = versions |> first()
print("Version:", latest.version)
print("Image:", latest.images |> first())

Returns a List of Records: {version, images}, where images is a List of URI strings.

Configuration

The BioContainers API URL is configurable via ~/.biolang/apis.yaml or the BIOLANG_BIOCONTAINERS_URL environment variable.

Builtin Reference

Practical Examples

Find Container Images for a Workflow

# Find containers for common variant calling tools
let tools = ["samtools", "bcftools", "gatk4", "bwa-mem2", "deepvariant"]

tools
  |> map(|name| {
    let versions = biocontainers_versions(name)
    let latest = versions |> first()
    { tool: name, version: latest.version, image: latest.images |> first() }
  })
  |> to_table()
  |> print()

Compare Tool Versions

# See how many versions are available for popular tools
biocontainers_popular(10)
  |> map(|t| { name: t.name, versions: t.version_count, latest: t.latest_version })
  |> sort(.versions)
  |> reverse()
  |> print()

Search and Inspect a Tool

# Find a tool and get its full details
let results = biocontainers_search("minimap2", 1)
let tool_name = results |> first() |> get("name")

# Get detailed info
let info = biocontainers_info(tool_name)
print("Tool:", info.name)
print("Description:", info.description)
print("Versions available:", info.version_count)

# List the 5 most recent versions
biocontainers_versions(tool_name)
  |> take(5)
  |> map(|v| { version: v.version, images: v.images |> len() })
  |> print()