External sources we sync from.

Each entry copies a single file (or generated artifact) from an upstream repo into content/ at a pinned SHA. Refresh with tsx scripts/sync-vendored-upstreams.ts. A build step, when present, runs in the upstream working tree before the copy and is deduped across entries.

• content/research/galaxy-collection-semantics.yml

  source

  $GALAXY/lib/galaxy/model/dataset_collections/types/collection_semantics.yml

  pinned

  7765fae934fb

  framing

  content/research/galaxy-collection-semantics.md

• content/research/galaxy-collection-semantics.upstream.myst

  source

  $GALAXY/doc/source/dev/collection_semantics.md

  pinned

  7765fae934fb

  framing

  content/research/galaxy-collection-semantics.md

• content/research/galaxy.xsd

  source

  $GALAXY/lib/galaxy/tool_util/xsd/galaxy.xsd

  pinned

  7765fae934fb

  framing

  content/research/galaxy-xsd.md

• content/research/datatypes_conf.xml.sample

  source

  $GALAXY/config/datatypes_conf.xml.sample

  pinned

  7765fae934fb

  framing

  content/research/galaxy-datatypes-conf.md

• content/research/gxformat2.schema.json

  source

  $GALAXY_TOOL_UTIL_TS/dist/structural-schemas/gxformat2.schema.json

  pinned

  7ae4ecd0ba8d

  framing

  content/research/gxformat2-schema.md

  build

  pnpm install --silent && pnpm -r build >/dev/null && mkdir -p dist/structural-schemas \
    && node packages/cli/dist/bin/gxwf.js structural-schema --format format2 \
         --output dist/structural-schemas/gxformat2.schema.json \
    && node packages/cli/dist/bin/gxwf.js structural-schema --format native \
         --output dist/structural-schemas/native-galaxy-workflow.schema.json

• content/research/native-galaxy-workflow.schema.json

  source

  $GALAXY_TOOL_UTIL_TS/dist/structural-schemas/native-galaxy-workflow.schema.json

  pinned

  7ae4ecd0ba8d

  framing

  content/research/galaxy-native-workflow-schema.md

  build

  pnpm install --silent && pnpm -r build >/dev/null && mkdir -p dist/structural-schemas \
    && node packages/cli/dist/bin/gxwf.js structural-schema --format format2 \
         --output dist/structural-schemas/gxformat2.schema.json \
    && node packages/cli/dist/bin/gxwf.js structural-schema --format native \
         --output dist/structural-schemas/native-galaxy-workflow.schema.json

• content/research/cwl-v1.2/cwl.yaml

  source

  https://raw.githubusercontent.com/common-workflow-language/cwl-v1.2/ae6899d159b5d62411f5f16d797f1d8e2176c5ba/json-schema/cwl.yaml

  pinned

  ae6899d159b5d62411f5f16d797f1d8e2176c5ba

  framing

  content/research/cwl-v1.2-schemas.md

• content/research/cwl-v1.2/CommonWorkflowLanguage.yml

  source

  https://raw.githubusercontent.com/common-workflow-language/cwl-v1.2/ae6899d159b5d62411f5f16d797f1d8e2176c5ba/CommonWorkflowLanguage.yml

  pinned

  ae6899d159b5d62411f5f16d797f1d8e2176c5ba

  framing

  content/research/cwl-v1.2-schemas.md

• content/research/cwl-v1.2/Process.yml

  source

  https://raw.githubusercontent.com/common-workflow-language/cwl-v1.2/ae6899d159b5d62411f5f16d797f1d8e2176c5ba/Process.yml

  pinned

  ae6899d159b5d62411f5f16d797f1d8e2176c5ba

  framing

  content/research/cwl-v1.2-schemas.md

• content/research/cwl-v1.2/CommandLineTool.yml

  source

  https://raw.githubusercontent.com/common-workflow-language/cwl-v1.2/ae6899d159b5d62411f5f16d797f1d8e2176c5ba/CommandLineTool.yml

  pinned

  ae6899d159b5d62411f5f16d797f1d8e2176c5ba

  framing

  content/research/cwl-v1.2-schemas.md

• content/research/cwl-v1.2/CommandLineTool-standalone.yml

  source

  https://raw.githubusercontent.com/common-workflow-language/cwl-v1.2/ae6899d159b5d62411f5f16d797f1d8e2176c5ba/CommandLineTool-standalone.yml

  pinned

  ae6899d159b5d62411f5f16d797f1d8e2176c5ba

  framing

  content/research/cwl-v1.2-schemas.md

• content/research/cwl-v1.2/Workflow.yml

  source

  https://raw.githubusercontent.com/common-workflow-language/cwl-v1.2/ae6899d159b5d62411f5f16d797f1d8e2176c5ba/Workflow.yml

  pinned

  ae6899d159b5d62411f5f16d797f1d8e2176c5ba

  framing

  content/research/cwl-v1.2-schemas.md

• content/research/cwl-v1.2/Operation.yml

  source

  https://raw.githubusercontent.com/common-workflow-language/cwl-v1.2/ae6899d159b5d62411f5f16d797f1d8e2176c5ba/Operation.yml

  pinned

  ae6899d159b5d62411f5f16d797f1d8e2176c5ba

  framing

  content/research/cwl-v1.2-schemas.md

• content/prompts/galaxy/custom-tool-critic.upstream.prompt

  source

  $GALAXY_DANNON/lib/galaxy/agents/prompts/custom_tool_critic.md

  pinned

  69d0c697b495

  framing

  content/prompts/galaxy/custom-tool-critic.md

• content/prompts/galaxy/custom-tool-structured.upstream.prompt

  source

  $GALAXY_DANNON/lib/galaxy/agents/prompts/custom_tool_structured.md

  pinned

  69d0c697b495

  framing

  content/prompts/galaxy/custom-tool-structured.md

galaxyproject/iwc cloned into workflow-fixtures/iwc-src/ at the pinned SHA, then cleaned + converted to gxformat2 under iwc-format2/ and reduced to topology-only views under iwc-skeletons/. Materialize with make fixtures-iwc fixtures-skeletons. Cited from surveys as $IWC_FORMAT2/... / $IWC_SKELETONS/.... Generated dirs are gitignored; nothing under content/ reads from them at build time.

ref

main

sha

deafc4876f2c

Pinned Nextflow pipeline clones used as research evidence for the summarize-nextflow Mold and adjacent gxwf skill work. Materialize with make fixtures-nextflow; verify pins with make fixtures-verify. Not used at site build time.

Authoring notes cite upstream files inline as $NAME/path/to/file.ext. The site rewrites these into clickable GitHub permalinks at build time using the repo + ref declared in common_paths.yml (gitignored, per-machine; falls back to the committed .sample). Not a sync — a binding.

• $GALAXY dev
  galaxyproject/galaxy
• $GALAXY_DANNON 69d0c697b495b7f16b1475c00c8bfbd7b9bfa85e
  dannon/galaxy
• $GALAXY_TOOL_UTIL_TS main
  jmchilton/galaxy-tool-util-ts
• $GXFORMAT2 main
  galaxyproject/gxformat2
• $IWC main
  galaxyproject/iwc
• $PLANEMO master
  galaxyproject/planemo
• $TOOLS_IUC main
  galaxyproject/tools-iuc