Install and run Foundry skills with Claude Code.
The Foundry casts each Mold into a self-contained skill, and assembles each Pipeline into a
runnable harness. Both are committed under casts/ and surfaced
as a Claude Code plugin marketplace. Install once; run a pipeline
end-to-end or invoke any cast skill directly.
- Pipelines
- 7
- Claude
- 25
- Casts
- 25
Install
/ Claude Code plugin marketplaceIn Claude Code, add the marketplace and install the plugin:
/plugin marketplace add galaxyproject/foundry
/plugin install foundry-skills@galaxy-workflow-foundrySkills are namespaced under the plugin. Invoke a cast skill in a session like:
/foundry-skills:summarize-nextflow
Or skip the marketplace and copy a single skill into ~/.claude/skills/:
git clone https://github.com/galaxyproject/foundry
cp -r foundry/casts/claude/skills/<name> ~/.claude/skills/<name>
Update later with /plugin update foundry-skills@galaxy-workflow-foundry.
Run a pipeline
/ how to run one end-to-end today
A Foundry pipeline is an ordered sequence of Molds that walks a source workflow to a target
workflow. You run one today via its assembled pipeline-* harness
skill — a stop-gap that invokes each phase's cast in order.
- Install the harness skills. They install like any Foundry cast skill —
via the Claude Code plugin marketplace or copied into
~/.claude/skills/. See Install. - Make the runtime available. Pipelines call out to
gxwf(schema/validation), Planemo (test execution), and the Foundry validators. Install these in the environment before a run that reaches the validate/test phases. - Invoke the harness for the pipeline you want. Each run gets its own
./<run-slug>/working directory, so artifacts stay namespaced and a second run won't clobber the first — the harness creates it before phase 1. - Optional run flags. Pass
--use-subagentsto run each cast phase in its own subagent (one per loop iteration) so the orchestrator's context stays small, and--checkpointtogit initthe run directory and commit after every phase — a per-step history for workflow-implementation visualizations. Both default off and compose.
Runnable harnesses
/ 7 runnable-
Path from a CWL Workflow to a Galaxy gxformat2 workflow. Lighter upstream extraction.
/foundry-skills:pipeline-cwl-to-galaxy11 phases · 10 auto · 1 manual · 1 loop
-
Interview-driven path to a Galaxy gxformat2 workflow through the shared freeform-summary handoff.
/foundry-skills:pipeline-interview-to-galaxy12 phases · 11 auto · 1 manual · 1 loop
-
Direct path from a Nextflow pipeline to a CWL Workflow + CommandLineTool set.
/foundry-skills:pipeline-nextflow-to-cwl12 phases · 2 auto · 10 manual · 3 loops
-
Direct path from a Nextflow pipeline to a Galaxy gxformat2 workflow.
/foundry-skills:pipeline-nextflow-to-galaxy12 phases · 10 auto · 2 manual · 1 loop
-
Direct path from a paper to a CWL Workflow + CommandLineTool set.
/foundry-skills:pipeline-paper-to-cwl11 phases · 1 auto · 10 manual · 3 loops
-
Direct path from a paper to a Galaxy gxformat2 workflow. No CWL intermediate.
/foundry-skills:pipeline-paper-to-galaxy12 phases · 10 auto · 2 manual · 1 loop
-
Interview-driven, edit-in-place modification of an existing Galaxy gxformat2 workflow via a reviewable change-set, reusing the per-step draft loop.
/foundry-skills:pipeline-update-interview-to-galaxy9 phases · 5 auto · 4 manual · 1 loop
Claude skills
/ 25 casts-
Advance the gxformat2 draft by one step: pick the next drafty step, resolve a wrapper, implement the step, and validate.
-
Author a new Galaxy user-defined tool YAML definition when discovery yields nothing acceptable.
-
Find nearest IWC exemplar(s) and surface a structural diff against the upstream Galaxy design briefs to guide template authoring.
-
Convert one nf-core module dir into a Galaxy tool wrapper (tool.xml + macros.xml + _provenance.yml + remote-URL <test> blocks).
-
Translate a CWL summary into a Galaxy data-flow design brief.
-
Map a CWL summary into a Galaxy workflow interface design brief.
-
gxformat2 skeleton with per-step TODOs from a CWL summary and prior Galaxy design briefs.
-
Triage failing Galaxy run outputs; classify the failure surface and capture evidence before recommending repairs.
-
Search the Tool Shed for an existing wrapper, drill from hit to a pinnable changeset, classify candidates, and recommend or fall through.
-
Search IWC fixtures and public sources for test data matching a data-flow shape.
-
Translate a free-form source summary into a Galaxy data-flow design brief.
-
Map a free-form source summary into a Galaxy workflow interface design brief.
-
gxformat2 skeleton with per-step TODOs from a free-form summary and Galaxy design brief.
-
Synthesize a Galaxy workflow test plan from a free-form summary and the Galaxy design briefs.
-
Convert an abstract step into a concrete gxformat2 step using a tool summary.
-
Assemble Galaxy workflow test fixtures and assertions.
-
Normalize a free-form user interview into the shared freeform-summary workflow handoff.
-
Translate a Nextflow summary into a Galaxy data-flow design brief.
-
Map a Nextflow summary into a Galaxy workflow interface design brief.
-
gxformat2 skeleton with per-step TODOs from a Nextflow summary and prior Galaxy design briefs.
-
Execute a workflow's tests via Planemo; emit structured pass/fail and outputs.
-
Validate and normalize a CWL Workflow tree, then emit a lightweight structured summary for downstream Galaxy translation.
-
Pull JSON schema, container, source, inputs/outputs for a Galaxy tool.
-
Read a Nextflow pipeline source tree (nf-core or ad-hoc DSL2) and emit a structured JSON summary for downstream translation Molds.
-
Run terminal gxwf validation on an assembled Galaxy workflow and classify workflow-level failures.