Foundry
Usage

Install and run Foundry skills with Claude Code or Codex.

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 one shared Agent Skills bundle with thin Claude Code and Codex plugin metadata. Install once in your runtime; run a pipeline end-to-end or invoke any cast skill directly.

Pipelines
7
Shared skills
33
Casts
33

Install

/ one bundle, two runtimes

Claude Code. Add the marketplace and install the plugin: 

/plugin marketplace add galaxyproject/foundry
/plugin install foundry-skills@galaxy-workflow-foundry

Skills are namespaced under the plugin. Invoke a cast skill in a session like: 

/foundry-skills:summarize-nextflow

Codex. Add the same repository marketplace and install the same plugin: 

codex plugin marketplace add galaxyproject/foundry
codex plugin add foundry-skills@galaxy-workflow-foundry

In Codex CLI or the IDE, run /skills or type $ to select a skill explicitly: 

$summarize-nextflow

Codex may also select a skill implicitly when your task matches its description.

Or skip plugin installation and copy a single skill into the runtime's user skill directory: 

git clone https://github.com/galaxyproject/foundry
cp -r foundry/casts/claude/skills/<name> ~/.claude/skills/<name>  # Claude Code
cp -r foundry/casts/claude/skills/<name> ~/.agents/skills/<name>  # Codex

Update Claude Code with /plugin update foundry-skills@galaxy-workflow-foundry. Refresh the Codex marketplace with codex plugin marketplace upgrade galaxy-workflow-foundry. Restart the runtime if updated skills do not appear.

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.

  1. Install the harness skills. They install like any Foundry cast skill through the Claude Code or Codex plugin metadata around the same shared bundle. See Install.
  2. 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.
  3. 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.
  4. Optional run flags. Pass --use-subagents to run each cast phase in its own subagent (one per loop iteration) so the orchestrator's context stays small, and --checkpoint to git init the run directory and commit after every phase — a per-step history for workflow-implementation visualizations. Both default off and compose.

Runnable harnesses

/ 7 runnable
  • pipeline-cwl-to-galaxy CWL → GALAXY →

    Path from a CWL Workflow to a Galaxy gxformat2 workflow. Lighter upstream extraction.

    Claude: /foundry-skills:pipeline-cwl-to-galaxy
Codex:  $pipeline-cwl-to-galaxy

    12 phases · 10 auto · 2 manual · 1 loop

  • pipeline-interview-to-galaxy INTERVIEW → GALAXY →

    Interview-driven path to a Galaxy gxformat2 workflow through the shared freeform-summary handoff.

    Claude: /foundry-skills:pipeline-interview-to-galaxy
Codex:  $pipeline-interview-to-galaxy

    12 phases · 11 auto · 1 manual · 1 loop

  • pipeline-nextflow-to-cwl NEXTFLOW → CWL →

    Direct path from a Nextflow pipeline to a CWL Workflow + CommandLineTool set.

    Claude: /foundry-skills:pipeline-nextflow-to-cwl
Codex:  $pipeline-nextflow-to-cwl

    12 phases · 2 auto · 10 manual · 3 loops

  • pipeline-nextflow-to-galaxy NEXTFLOW → GALAXY →

    Direct path from a Nextflow pipeline to a Galaxy gxformat2 workflow.

    Claude: /foundry-skills:pipeline-nextflow-to-galaxy
Codex:  $pipeline-nextflow-to-galaxy

    13 phases · 12 auto · 1 manual · 1 loop

  • pipeline-paper-to-cwl PAPER → CWL →

    Direct path from a paper to a CWL Workflow + CommandLineTool set.

    Claude: /foundry-skills:pipeline-paper-to-cwl
Codex:  $pipeline-paper-to-cwl

    11 phases · 1 auto · 10 manual · 3 loops

  • pipeline-paper-to-galaxy PAPER → GALAXY →

    Direct path from a paper to a Galaxy gxformat2 workflow. No CWL intermediate.

    Claude: /foundry-skills:pipeline-paper-to-galaxy
Codex:  $pipeline-paper-to-galaxy

    12 phases · 10 auto · 2 manual · 1 loop

  • pipeline-update-interview-to-galaxy UPDATE-INTERVIEW → GALAXY →

    Interview-driven, edit-in-place modification of an existing Galaxy gxformat2 workflow via a reviewable change-set, reusing the per-step draft loop.

    Claude: /foundry-skills:pipeline-update-interview-to-galaxy
Codex:  $pipeline-update-interview-to-galaxy

    9 phases · 9 auto · 0 manual · 1 loop

Shared Agent Skills

/ 33 casts