SEAB-7746 Prototype the remaining GA4GH TRS V2 tools

[denis-yuen]

Description
A prototype for SEAB-7746, to get a sense of what is possible. It adds the remaining GA4GH TRS V2 tools from the ga4gh-mcp tutorials (list_tools, search_tools, get_tool, list_tool_versions, get_tool_version, get_tool_descriptor, get_tool_descriptor_by_path, get_tool_files, get_tool_tests, get_tool_containerfile), which gives this server feature parity with them. Beyond the tutorials, list_tools/search_tools report totals and take a summary option that makes responses about 17× smaller. Notebooks and services are supported, and requests send a dockstore-mcp/<git ref> User-Agent. The TRS filters are case-sensitive substring matches, so a performant search still needs SEAB-7733.

Review Instructions
Run make check, then point an MCP client at a local server (DOCKSTORE_MCP_DOCKSTORE_URL=https://dockstore.org make run) and try prompts from the ga4gh-mcp tutorials; a sample run is in a comment below. Stacked on #5.

Issue
SEAB-7746 (https://ucsc-cgl.atlassian.net/browse/SEAB-7746). Follow-up: SEAB-7733 (https://ucsc-cgl.atlassian.net/browse/SEAB-7733).

Security and Privacy

None

• Security and Privacy assessed

e.g. Does this change...

• Any user data we collect, or data location?
• Access control, authentication or authorization?
• Encryption features?

Please make sure that you've checked the following before submitting your pull request. Thanks!

• Check that you pass the basic style checks and unit tests by running make check
• Ensure that the PR targets the correct branch. Check the milestone or fix version of the ticket.
• If you are changing dependencies, check the Snyk status check or the dashboard to ensure you are not introducing new high/critical vulnerabilities
• Assume that arguments passed to a tool can be malicious, and sanitize and/or check for Denial of Service type values, e.g., massive sizes
• Do not log or return secrets/credentials in a tool's response, error message, or debug output
• If this PR is for a user-facing feature, create and link a documentation ticket for this feature (usually in the same milestone as the linked issue). Style points if you create a documentation PR directly and link that instead.

🤖 Generated with Claude Code

[denis-yuen]

This comment was generated by Claude (Claude Code): a sample run of this branch against Dockstore production, via a local server (local_mcp_2_dockstore_prod).

Prompt:

Get me a list of RNAseq workflows from Dockstore uusing local_mcp_2_dockstore_prod and group by language, but also find out how many versions of each workflow there are

How it was answered: nine search_tools calls with tool_class=Workflow and summary=true. The TRS filters are case-sensitive, so each call used a different spelling in name or toolname: rnaseq, RNAseq, rna-seq, RNASeq, and RNA-seq for toolname only. Results were deduplicated by TRS id. Workflows that only mention RNA-seq in their README (91 of them) are not included, and doing better is the job of SEAB-7733.

---

There are 57 RNA-seq workflows with 801 versions between them, sorted by version count within each language.

A "version" is any Git branch or tag Dockstore has picked up, so busy repositories inflate the counts:

• WARP rnaseq_aou: its 323 versions are every branch and tag in the whole WARP monorepo, not releases of this workflow.
• AoU-Multiomics rnaseqc2_aggregate_batched: most of its 54 are codex/* feature branches.
• nf-core pipelines: also count dev, template and feature branches alongside their numbered releases.

WDL (41 workflows, 516 versions)

Workflow	Versions
broadinstitute/warp/rnaseq_aou	323
AoU-Multiomics-Analysis/prepare_QTL/rnaseqc2_aggregate_batched	54
f73chen/rnaSeqQC/RNASeqQC	21
ENCODE-DCC/mirna-seq-pipeline_wdl_checker	13
gatk-workflows/gatk4-rnaseq-germline-snps-indels	8
hacchy1983/rna-seq-pipeline	5
richardslab/gtex-pipeline/CombineRNASeqc2Files	5
ENCODE-DCC/rna-seq-pipeline	4
gatk-workflows/gatk3-4-rnaseq-germline-snps-indels	4
richardslab/gtex-pipeline/CreateRNASeqQCSampleName	4
ENCODE-DCC/mirna-seq-pipeline	2
Kayla-Morrell/AnVILBulkRNASeq	2
WhiteLabGenomics/TerraPipelines_BulkRNAseq/bulkRNA_workflow	2
broadinstitute/MDL-workflows/rnaseqc2	2
broadinstitute/depmap_omics/rnaseq_mutect2_tumor_only	2
chunjie-sam-liu/rna-seq-quant-wdl	2

These 25 have 1 version each:

• aarong/rnaseqc
• IfrahTariq/bulkRNA_workflow
• Mo7ammedFarahat/RNASeq_WDL
• ParkerICI/single_cell_workflows/rnaseq
• TrinityCTAT/RNA-SeQC2-long
• broadinstitute/depmap_omics/RNA_stranded_rsem_rnaseqc2
• broadinstitute/gpp-rnaseq-analysis: RNA_aggregate, RNA_pipeline, rsem_depmap
• broadinstitute/rna_seq_sars_cov_2/trinityrnaseq
• broadinstitute/warp: aggregate_rnaseqc2, rnaseqc2_aggregate_batched
• getwilds/ww-rnaseq
• gulhanlab/GTEx-RNAseq-pipeline: GTEx-RNAseq-BAM, GTEx-RNAseq-FASTQ, GenerateRSEMReference, GenerateSTARIndex, samtools_idx
• lux563624348/salmon-rnaseq-wdl, plus its checker
• qinqian/depmap_omics: RNA_stranded_rsem_rnaseqc2, rnaseq_mutect2_tumor_only
• sidwekhande/RNA-seq
• thouis/gatk4-rnaseq-germline-snps-indels
• welch-lab/STEAMER-RNAseq

Nextflow (7 workflows, 172 versions)

Workflow	Versions
nf-core/rnaseq	87
nf-core/smrnaseq	33
nf-core/scrnaseq	28
nf-core/dualrnaseq	14
nextflow-io/rnaseq-nf	5
denis-yuen/rnaseq	4
Vivian-chen16/RNAseq-QTL-wf	1

Galaxy (5 workflows, 68 versions)

Workflow	Versions
iwc-workflows/rnaseq-pe	17
iwc-workflows/rnaseq-sr	15
iwc-workflows/scrna-seq-fastq-to-matrix-10x-cellplex	12
iwc-workflows/scrna-seq-fastq-to-matrix-10x-v3	12
iwc-workflows/rnaseq-de	12

CWL (4 workflows, 83 versions)

Workflow	Versions
hubmapconsortium/salmon-rnaseq	78
SciDAP/workflows/xenbase-rnaseq-se	2
sevenbridges-openworkflows/Broad-Best-Practice-rnaseq-germline-snps-indels	2
sbg/sbg_dockstore_tools/gtex-rna-seq-pipeline	1

No workflow is published in more than one language. The TRS API doesn't say whether a version is a branch or a tag, so release-only counts would need a heuristic based on version names.

[denis-yuen]

This supports the ability to tag the user agent with the version (tag or branch) that this repo is on

[denis-yuen]

I asked for this option to reduce the response size when the contents are not useful for the query (like in the example comment)

[denis-yuen]

merged into #12 while reducing tools