Example: Tool Discovery

BioLedger can discover tools from external repositories — the Galaxy Tool Shed, nf-core modules, and Snakemake wrappers — and run them with their native workflow engines. No translation to BioLedger specs is required.

Files in this directory

trimmomatic.nf — Example Nextflow DSL2 module (kept as reference; not importable as a BioLedger spec)
isatab/ — Complete ISA-Tab dataset directory with synthetic test data:
i_investigation.txt — Investigation metadata
s_study.txt — Study with one sample
a_assay.txt — Sequencing assay pointing to the FASTQ
sample.fastq — Tiny synthetic FASTQ file (4 reads)

Search for tools

Use bioledger tool search to find tools in the Galaxy Tool Shed and nf-core modules:

# Search both sources
bioledger tool search "fastqc"

# Search only the Galaxy Tool Shed
bioledger tool search "bwa" --source toolshed

# Search only nf-core modules
bioledger tool search "samtools" --source nfcore

Results show tool name, description, and repository information.

Run discovered tools in a session

Inside an interactive session, the agent can search all three repositories (search_toolshed, search_nfcore, search_snakemake_wrappers — the last has no CLI --source equivalent yet) and run discovered tools directly:

bioledger session new tool-discovery-test
bioledger resume tool-discovery-test

you> load examples/tool_discovery/isatab/
Loaded dataset "Sample FastQC Test Dataset"
  Samples: 1
  Organisms: Homo sapiens
  File formats: fastq

you> search the tool shed for fastqc
assistant> Tool Shed results:
  fastqc: FastQC — Read Quality reports (repo: iuc/fastqc)

you> run the fastqc tool from the tool shed on the sample
assistant> Submitted discovered tool fastqc as job abc123.
           Source: toolshed:iuc/fastqc. Type 'status' to check progress.

How it works: - Galaxy Tool Shed tools → downloaded tool XML is run by planemo run with a generated job.yml for inputs/params. - nf-core modules → installed via nf-core modules install, then wrapped in a generated main.nf + nextflow.config and run by Nextflow. - Snakemake wrappers → downloaded wrapper plus a generated Snakefile using the native wrapper: directive, run by Snakemake. - Revision pinning → append @<revision> to the discovered-source string (toolshed:<owner>/<repo>@<rev>, nfcore:<subdir>@<sha>, snakemake:<path>@<tag>). The resolved revision is recorded on the ledger entry for reproducibility.

Import a BioLedger YAML spec

If you have a BioLedger tool spec (.bioledger.yaml), you can import it to the local store:

bioledger tool import specs/samtools_sort.bioledger.yaml

Example: Tool Discovery

Files in this directory

Search for tools

Run discovered tools in a session

Import a BioLedger YAML spec

See also