@galaxyproject/orbit 0.0.0 → 0.9.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CHANGELOG.md +123 -0
- package/LICENSE +21 -0
- package/README.md +760 -5
- package/bin/legacy-mcp-config.js +363 -0
- package/bin/orbit.js +810 -0
- package/bin/pi-extension-path.d.ts +4 -0
- package/bin/pi-extension-path.js +44 -0
- package/bin/provider-auth.d.ts +22 -0
- package/bin/provider-auth.js +77 -0
- package/bin/thinking-pref.js +38 -0
- package/bin/update-check.d.ts +15 -0
- package/bin/update-check.js +137 -0
- package/extensions/cli-update/index.ts +32 -0
- package/extensions/orbit/activity-hooks.ts +141 -0
- package/extensions/orbit/activity.ts +116 -0
- package/extensions/orbit/agent-dir.ts +11 -0
- package/extensions/orbit/auto-resume.ts +352 -0
- package/extensions/orbit/config.ts +3 -0
- package/extensions/orbit/confusables.ts +1 -0
- package/extensions/orbit/context.ts +957 -0
- package/extensions/orbit/dashboard-commands.ts +191 -0
- package/extensions/orbit/dashboard-store.ts +473 -0
- package/extensions/orbit/dashboard-tools.ts +1185 -0
- package/extensions/orbit/empty-completion.ts +99 -0
- package/extensions/orbit/evidence-gate.ts +1276 -0
- package/extensions/orbit/evidence-override-command.ts +294 -0
- package/extensions/orbit/exec-guard/bash-risk.ts +1408 -0
- package/extensions/orbit/exec-guard/gate.ts +181 -0
- package/extensions/orbit/exec-guard/guardian-config.ts +54 -0
- package/extensions/orbit/exec-guard/index.ts +1 -0
- package/extensions/orbit/exec-guard/model-tier.ts +36 -0
- package/extensions/orbit/exec-guard/path-jail.ts +54 -0
- package/extensions/orbit/exec-guard/policy.ts +342 -0
- package/extensions/orbit/exec-guard/runtime-state.ts +15 -0
- package/extensions/orbit/exec-guard/sensitive-read.ts +525 -0
- package/extensions/orbit/exec-guard/types.ts +42 -0
- package/extensions/orbit/execution-commands.ts +134 -0
- package/extensions/orbit/feedback-command.ts +81 -0
- package/extensions/orbit/feedback.ts +96 -0
- package/extensions/orbit/galaxy-api.test.ts +122 -0
- package/extensions/orbit/galaxy-api.ts +606 -0
- package/extensions/orbit/galaxy-artifact-link-guidance.ts +5 -0
- package/extensions/orbit/galaxy-destructive-gate.ts +113 -0
- package/extensions/orbit/galaxy-enrich.ts +1108 -0
- package/extensions/orbit/galaxy-failure.ts +101 -0
- package/extensions/orbit/galaxy-fixture.ts +126 -0
- package/extensions/orbit/galaxy-history-guard.ts +233 -0
- package/extensions/orbit/galaxy-job-block.ts +347 -0
- package/extensions/orbit/galaxy-job-ops.ts +288 -0
- package/extensions/orbit/galaxy-live-source.ts +929 -0
- package/extensions/orbit/galaxy-markdown-adapter.ts +248 -0
- package/extensions/orbit/galaxy-op-policy.ts +332 -0
- package/extensions/orbit/galaxy-ops-tools.ts +326 -0
- package/extensions/orbit/galaxy-output-store.ts +80 -0
- package/extensions/orbit/galaxy-output.ts +346 -0
- package/extensions/orbit/galaxy-page-binding.ts +222 -0
- package/extensions/orbit/galaxy-page-markdown-guidance.ts +15 -0
- package/extensions/orbit/galaxy-page-ops.ts +159 -0
- package/extensions/orbit/galaxy-page-sync.test.ts +417 -0
- package/extensions/orbit/galaxy-page-sync.ts +318 -0
- package/extensions/orbit/galaxy-pages-api.ts +203 -0
- package/extensions/orbit/galaxy-pages-sync.ts +409 -0
- package/extensions/orbit/galaxy-poll-guard.ts +189 -0
- package/extensions/orbit/galaxy-poller.ts +706 -0
- package/extensions/orbit/galaxy-provenance.ts +623 -0
- package/extensions/orbit/galaxy-reconcile.ts +956 -0
- package/extensions/orbit/galaxy-recovery.ts +176 -0
- package/extensions/orbit/galaxy-repeat-guard.ts +55 -0
- package/extensions/orbit/galaxy-submission-capture.ts +707 -0
- package/extensions/orbit/galaxy-submission.ts +502 -0
- package/extensions/orbit/galaxy-tool-source.ts +78 -0
- package/extensions/orbit/galaxy-tool-wrap.ts +234 -0
- package/extensions/orbit/galaxy-udt-block.ts +127 -0
- package/extensions/orbit/galaxy-upload-tus.ts +334 -0
- package/extensions/orbit/galaxy-upload.ts +300 -0
- package/extensions/orbit/galaxy-version-capture.ts +65 -0
- package/extensions/orbit/git.ts +173 -0
- package/extensions/orbit/harness-block-fields.ts +597 -0
- package/extensions/orbit/index.ts +593 -0
- package/extensions/orbit/init-gate.ts +284 -0
- package/extensions/orbit/instructions-command.ts +136 -0
- package/extensions/orbit/invocation-failure-hint.ts +57 -0
- package/extensions/orbit/iwc-plan-check.ts +94 -0
- package/extensions/orbit/lesson-command.ts +303 -0
- package/extensions/orbit/lesson-hint.ts +245 -0
- package/extensions/orbit/lesson-nudge.ts +106 -0
- package/extensions/orbit/lessons/compose.ts +177 -0
- package/extensions/orbit/lessons/counters.ts +120 -0
- package/extensions/orbit/lessons/enabled.ts +116 -0
- package/extensions/orbit/lessons/matcher.ts +346 -0
- package/extensions/orbit/lessons/paths.ts +286 -0
- package/extensions/orbit/lessons/pi-event-contract.ts +105 -0
- package/extensions/orbit/lessons/propose-replay.ts +103 -0
- package/extensions/orbit/lessons/propose-tool.ts +222 -0
- package/extensions/orbit/lessons/propose.ts +502 -0
- package/extensions/orbit/lessons/replay.ts +89 -0
- package/extensions/orbit/lessons/reproduction-index.ts +83 -0
- package/extensions/orbit/lessons/search-tool.ts +99 -0
- package/extensions/orbit/lessons/search.ts +136 -0
- package/extensions/orbit/lessons/store.ts +415 -0
- package/extensions/orbit/lessons/text.ts +36 -0
- package/extensions/orbit/lessons/types.ts +69 -0
- package/extensions/orbit/lessons/user-dir.ts +24 -0
- package/extensions/orbit/lessons/user-lesson.ts +88 -0
- package/extensions/orbit/lessons/wrapper.ts +61 -0
- package/extensions/orbit/lessons-command.ts +147 -0
- package/extensions/orbit/local-exec.ts +39 -0
- package/extensions/orbit/mcp-output.ts +179 -0
- package/extensions/orbit/mcp-servers.test.ts +24 -0
- package/extensions/orbit/mcp-servers.ts +25 -0
- package/extensions/orbit/model-script.ts +351 -0
- package/extensions/orbit/notebook-anchors.ts +342 -0
- package/extensions/orbit/notebook-writer.ts +863 -0
- package/extensions/orbit/observation-allowlists.ts +1109 -0
- package/extensions/orbit/observation-replay.ts +148 -0
- package/extensions/orbit/observation-triggers.ts +563 -0
- package/extensions/orbit/observation-ui.ts +175 -0
- package/extensions/orbit/observations-command.ts +421 -0
- package/extensions/orbit/observations-config.ts +200 -0
- package/extensions/orbit/observations.ts +1381 -0
- package/extensions/orbit/profiles.ts +270 -0
- package/extensions/orbit/progress-updates.ts +95 -0
- package/extensions/orbit/proposal-commands.ts +882 -0
- package/extensions/orbit/provenance-fs-file.ts +59 -0
- package/extensions/orbit/provenance-fs.ts +32 -0
- package/extensions/orbit/provenance-memory-fs.ts +59 -0
- package/extensions/orbit/record-store-file.ts +177 -0
- package/extensions/orbit/record-store-page.ts +77 -0
- package/extensions/orbit/record-store-seam.ts +47 -0
- package/extensions/orbit/record-store.ts +149 -0
- package/extensions/orbit/registry-carrier.ts +107 -0
- package/extensions/orbit/registry-eligibility.ts +95 -0
- package/extensions/orbit/registry-evaluation.ts +403 -0
- package/extensions/orbit/registry-evaluator.ts +519 -0
- package/extensions/orbit/registry-import.ts +91 -0
- package/extensions/orbit/registry-lock.ts +221 -0
- package/extensions/orbit/registry-memory-fs.ts +42 -0
- package/extensions/orbit/registry-page-carrier.ts +103 -0
- package/extensions/orbit/registry-proposal.ts +1348 -0
- package/extensions/orbit/registry-runtime.ts +234 -0
- package/extensions/orbit/registry-schema.ts +735 -0
- package/extensions/orbit/registry-submitter.ts +59 -0
- package/extensions/orbit/registry-templates.ts +346 -0
- package/extensions/orbit/registry.ts +476 -0
- package/extensions/orbit/sandbox/index.ts +120 -0
- package/extensions/orbit/sandbox/sandbox-bash.ts +93 -0
- package/extensions/orbit/sandbox/sandbox-config.ts +87 -0
- package/extensions/orbit/sandbox/sandbox-init-message.ts +28 -0
- package/extensions/orbit/secret-redaction.ts +247 -0
- package/extensions/orbit/session-index/cwd.ts +18 -0
- package/extensions/orbit/session-index/db.ts +56 -0
- package/extensions/orbit/session-index/indexer.ts +154 -0
- package/extensions/orbit/session-index/is-enabled.ts +17 -0
- package/extensions/orbit/session-index/parse.ts +254 -0
- package/extensions/orbit/session-index/query.ts +209 -0
- package/extensions/orbit/session-index/schema.ts +72 -0
- package/extensions/orbit/session-index/tools.ts +152 -0
- package/extensions/orbit/session-lifecycle.ts +321 -0
- package/extensions/orbit/skill-triggers.ts +159 -0
- package/extensions/orbit/skills-command.ts +48 -0
- package/extensions/orbit/skills-discovery.ts +435 -0
- package/extensions/orbit/skills.ts +84 -0
- package/extensions/orbit/sra-import-gate.ts +77 -0
- package/extensions/orbit/state.ts +265 -0
- package/extensions/orbit/submission-replay.ts +147 -0
- package/extensions/orbit/sync-command.ts +157 -0
- package/extensions/orbit/teams/critic-parser.ts +93 -0
- package/extensions/orbit/teams/dispatcher.ts +210 -0
- package/extensions/orbit/teams/is-enabled.ts +22 -0
- package/extensions/orbit/teams/tool.ts +187 -0
- package/extensions/orbit/teams/types.ts +57 -0
- package/extensions/orbit/teams/validate.ts +42 -0
- package/extensions/orbit/tester-id-command.ts +133 -0
- package/extensions/orbit/tools-sync.ts +279 -0
- package/extensions/orbit/tools.ts +1300 -0
- package/extensions/orbit/types.ts +41 -0
- package/extensions/orbit/ui-bridge.ts +55 -0
- package/extensions/orbit/ulid.ts +60 -0
- package/extensions/orbit/user-instructions.ts +388 -0
- package/extensions/orbit/vendor/skills/_catalog.json +68 -0
- package/extensions/orbit/vendor/skills/_manifest.json +1106 -0
- package/extensions/orbit/vendor/skills/advance-galaxy-draft-step/SKILL.md +112 -0
- package/extensions/orbit/vendor/skills/advance-galaxy-draft-step/_provenance.json +218 -0
- package/extensions/orbit/vendor/skills/advance-galaxy-draft-step/_required_tools.json +33 -0
- package/extensions/orbit/vendor/skills/advance-galaxy-draft-step/_verify.json +4 -0
- package/extensions/orbit/vendor/skills/advance-galaxy-draft-step/references/cli/add.json +50 -0
- package/extensions/orbit/vendor/skills/advance-galaxy-draft-step/references/cli/draft-extract.json +51 -0
- package/extensions/orbit/vendor/skills/advance-galaxy-draft-step/references/cli/draft-next-step.json +42 -0
- package/extensions/orbit/vendor/skills/advance-galaxy-draft-step/references/cli/draft-validate.json +140 -0
- package/extensions/orbit/vendor/skills/advance-galaxy-draft-step/references/cli/list.json +32 -0
- package/extensions/orbit/vendor/skills/advance-galaxy-draft-step/references/notes/galaxy-tool-job-failure-reference.md +137 -0
- package/extensions/orbit/vendor/skills/advance-galaxy-draft-step/references/notes/open-requirements-ledger.md +173 -0
- package/extensions/orbit/vendor/skills/advance-galaxy-draft-step/references/schemas/galaxy-tool-summary.schema.json +175 -0
- package/extensions/orbit/vendor/skills/advance-galaxy-draft-step/references/schemas/galaxy-workflow-draft.schema.json +2727 -0
- package/extensions/orbit/vendor/skills/apply-galaxy-workflow-changeset/SKILL.md +82 -0
- package/extensions/orbit/vendor/skills/apply-galaxy-workflow-changeset/_provenance.json +133 -0
- package/extensions/orbit/vendor/skills/apply-galaxy-workflow-changeset/_required_tools.json +16 -0
- package/extensions/orbit/vendor/skills/apply-galaxy-workflow-changeset/_verify.json +4 -0
- package/extensions/orbit/vendor/skills/apply-galaxy-workflow-changeset/references/cli/draft-validate.json +140 -0
- package/extensions/orbit/vendor/skills/apply-galaxy-workflow-changeset/references/notes/galaxy-workflow-draft-format.md +135 -0
- package/extensions/orbit/vendor/skills/apply-galaxy-workflow-changeset/references/notes/open-requirements-ledger.md +173 -0
- package/extensions/orbit/vendor/skills/apply-galaxy-workflow-changeset/references/schemas/galaxy-workflow-draft.schema.json +2727 -0
- package/extensions/orbit/vendor/skills/changeset-to-galaxy-test-plan/SKILL.md +84 -0
- package/extensions/orbit/vendor/skills/changeset-to-galaxy-test-plan/_provenance.json +166 -0
- package/extensions/orbit/vendor/skills/changeset-to-galaxy-test-plan/_verify.json +29 -0
- package/extensions/orbit/vendor/skills/changeset-to-galaxy-test-plan/references/notes/galaxy-workflow-testability-design.md +136 -0
- package/extensions/orbit/vendor/skills/changeset-to-galaxy-test-plan/references/notes/iwc-shortcuts-anti-patterns.md +357 -0
- package/extensions/orbit/vendor/skills/changeset-to-galaxy-test-plan/references/notes/iwc-test-data-conventions.md +308 -0
- package/extensions/orbit/vendor/skills/changeset-to-galaxy-test-plan/references/notes/planemo-asserts-idioms.md +246 -0
- package/extensions/orbit/vendor/skills/changeset-to-galaxy-test-plan/references/notes/planemo-workflow-test-architecture.md +151 -0
- package/extensions/orbit/vendor/skills/changeset-to-galaxy-test-plan/references/schemas/galaxy-workflow-test-plan.schema.json +552 -0
- package/extensions/orbit/vendor/skills/changeset-to-galaxy-test-plan/references/schemas/summary-galaxy-workflow.schema.json +687 -0
- package/extensions/orbit/vendor/skills/changeset-to-galaxy-test-plan/references/schemas/tests-format.schema.json +7328 -0
- package/extensions/orbit/vendor/skills/compare-against-iwc-exemplar/SKILL.md +127 -0
- package/extensions/orbit/vendor/skills/compare-against-iwc-exemplar/_provenance.json +198 -0
- package/extensions/orbit/vendor/skills/compare-against-iwc-exemplar/_required_tools.json +16 -0
- package/extensions/orbit/vendor/skills/compare-against-iwc-exemplar/_verify.json +4 -0
- package/extensions/orbit/vendor/skills/compare-against-iwc-exemplar/references/cli/convert.json +123 -0
- package/extensions/orbit/vendor/skills/compare-against-iwc-exemplar/references/notes/galaxy-data-flow-draft-contract.md +129 -0
- package/extensions/orbit/vendor/skills/compare-against-iwc-exemplar/references/notes/iwc-shortcuts-anti-patterns.md +357 -0
- package/extensions/orbit/vendor/skills/compare-against-iwc-exemplar/references/notes/iwc-test-data-conventions.md +308 -0
- package/extensions/orbit/vendor/skills/compare-against-iwc-exemplar/references/notes/open-requirements-ledger.md +173 -0
- package/extensions/orbit/vendor/skills/debug-galaxy-workflow-output/SKILL.md +73 -0
- package/extensions/orbit/vendor/skills/debug-galaxy-workflow-output/_provenance.json +160 -0
- package/extensions/orbit/vendor/skills/debug-galaxy-workflow-output/_verify.json +4 -0
- package/extensions/orbit/vendor/skills/debug-galaxy-workflow-output/references/notes/galaxy-collection-semantics.md +43 -0
- package/extensions/orbit/vendor/skills/debug-galaxy-workflow-output/references/notes/galaxy-collection-semantics.yml +1250 -0
- package/extensions/orbit/vendor/skills/debug-galaxy-workflow-output/references/notes/galaxy-tool-job-failure-reference.md +137 -0
- package/extensions/orbit/vendor/skills/debug-galaxy-workflow-output/references/notes/galaxy-workflow-invocation-failure-reference.md +138 -0
- package/extensions/orbit/vendor/skills/debug-galaxy-workflow-output/references/notes/iwc-shortcuts-anti-patterns.md +357 -0
- package/extensions/orbit/vendor/skills/debug-galaxy-workflow-output/references/notes/nextflow-operators-to-galaxy-collection-recipes.md +98 -0
- package/extensions/orbit/vendor/skills/debug-galaxy-workflow-output/references/notes/planemo-asserts-idioms.md +246 -0
- package/extensions/orbit/vendor/skills/debug-galaxy-workflow-output/references/notes/planemo-workflow-test-architecture.md +151 -0
- package/extensions/orbit/vendor/skills/discover-shed-tool/SKILL.md +174 -0
- package/extensions/orbit/vendor/skills/discover-shed-tool/_provenance.json +130 -0
- package/extensions/orbit/vendor/skills/discover-shed-tool/_required_tools.json +18 -0
- package/extensions/orbit/vendor/skills/discover-shed-tool/_verify.json +17 -0
- package/extensions/orbit/vendor/skills/discover-shed-tool/references/cli/tool-revisions.json +48 -0
- package/extensions/orbit/vendor/skills/discover-shed-tool/references/cli/tool-search.json +95 -0
- package/extensions/orbit/vendor/skills/discover-shed-tool/references/cli/tool-versions.json +39 -0
- package/extensions/orbit/vendor/skills/discover-shed-tool/references/notes/component-tool-shed-search.md +230 -0
- package/extensions/orbit/vendor/skills/discover-shed-tool/references/schemas/galaxy-tool-discovery.schema.json +231 -0
- package/extensions/orbit/vendor/skills/implement-galaxy-workflow-test/SKILL.md +93 -0
- package/extensions/orbit/vendor/skills/implement-galaxy-workflow-test/_provenance.json +201 -0
- package/extensions/orbit/vendor/skills/implement-galaxy-workflow-test/_required_tools.json +28 -0
- package/extensions/orbit/vendor/skills/implement-galaxy-workflow-test/_verify.json +17 -0
- package/extensions/orbit/vendor/skills/implement-galaxy-workflow-test/references/cli/planemo.md +44 -0
- package/extensions/orbit/vendor/skills/implement-galaxy-workflow-test/references/cli/validate-tests.json +40 -0
- package/extensions/orbit/vendor/skills/implement-galaxy-workflow-test/references/notes/galaxy-workflow-testability-design.md +136 -0
- package/extensions/orbit/vendor/skills/implement-galaxy-workflow-test/references/notes/iwc-shortcuts-anti-patterns.md +357 -0
- package/extensions/orbit/vendor/skills/implement-galaxy-workflow-test/references/notes/iwc-test-data-conventions.md +308 -0
- package/extensions/orbit/vendor/skills/implement-galaxy-workflow-test/references/notes/planemo-asserts-idioms.md +246 -0
- package/extensions/orbit/vendor/skills/implement-galaxy-workflow-test/references/notes/planemo-workflow-test-architecture.md +151 -0
- package/extensions/orbit/vendor/skills/implement-galaxy-workflow-test/references/schemas/galaxy-workflow-test-plan.schema.json +552 -0
- package/extensions/orbit/vendor/skills/implement-galaxy-workflow-test/references/schemas/tests-format.schema.json +7328 -0
- package/extensions/orbit/vendor/skills/interview-to-galaxy-workflow-changeset/SKILL.md +81 -0
- package/extensions/orbit/vendor/skills/interview-to-galaxy-workflow-changeset/_provenance.json +93 -0
- package/extensions/orbit/vendor/skills/interview-to-galaxy-workflow-changeset/_verify.json +17 -0
- package/extensions/orbit/vendor/skills/interview-to-galaxy-workflow-changeset/references/notes/open-requirements-ledger.md +173 -0
- package/extensions/orbit/vendor/skills/interview-to-galaxy-workflow-changeset/references/schemas/summary-galaxy-workflow.schema.json +687 -0
- package/extensions/orbit/vendor/skills/pipeline-update-interview-to-galaxy/SKILL.md +81 -0
- package/extensions/orbit/vendor/skills/pipeline-update-interview-to-galaxy/_assembly.json +23 -0
- package/extensions/orbit/vendor/skills/run-workflow-test/SKILL.md +79 -0
- package/extensions/orbit/vendor/skills/run-workflow-test/_provenance.json +125 -0
- package/extensions/orbit/vendor/skills/run-workflow-test/_required_tools.json +28 -0
- package/extensions/orbit/vendor/skills/run-workflow-test/_verify.json +4 -0
- package/extensions/orbit/vendor/skills/run-workflow-test/references/cli/planemo.md +44 -0
- package/extensions/orbit/vendor/skills/run-workflow-test/references/cli/validate-tests.json +40 -0
- package/extensions/orbit/vendor/skills/run-workflow-test/references/notes/galaxy-workflow-invocation-failure-reference.md +138 -0
- package/extensions/orbit/vendor/skills/run-workflow-test/references/notes/planemo-asserts-idioms.md +246 -0
- package/extensions/orbit/vendor/skills/run-workflow-test/references/notes/planemo-workflow-test-architecture.md +151 -0
- package/extensions/orbit/vendor/skills/run-workflow-test/references/schemas/tests-format.schema.json +7328 -0
- package/extensions/orbit/vendor/skills/skills/LICENSE +21 -0
- package/extensions/orbit/vendor/skills/skills/collection-manipulation/README.md +39 -0
- package/extensions/orbit/vendor/skills/skills/collection-manipulation/SKILL.md +892 -0
- package/extensions/orbit/vendor/skills/skills/collection-manipulation/references/api-patterns.md +927 -0
- package/extensions/orbit/vendor/skills/skills/collection-manipulation/references/apply-rules.md +1482 -0
- package/extensions/orbit/vendor/skills/skills/collection-manipulation/references/test-patterns.md +996 -0
- package/extensions/orbit/vendor/skills/skills/collection-manipulation/references/tools.md +609 -0
- package/extensions/orbit/vendor/skills/skills/galaxy-data-libraries/SKILL.md +170 -0
- package/extensions/orbit/vendor/skills/skills/galaxy-integration/README.md +162 -0
- package/extensions/orbit/vendor/skills/skills/galaxy-integration/SKILL.md +99 -0
- package/extensions/orbit/vendor/skills/skills/galaxy-integration/examples/README.md +119 -0
- package/extensions/orbit/vendor/skills/skills/galaxy-integration/examples/tool-checking.md +419 -0
- package/extensions/orbit/vendor/skills/skills/galaxy-integration/examples/workflow-testing.md +617 -0
- package/extensions/orbit/vendor/skills/skills/galaxy-integration/galaxy-integration.md +614 -0
- package/extensions/orbit/vendor/skills/skills/galaxy-integration/jupyterlite/SKILL.md +144 -0
- package/extensions/orbit/vendor/skills/skills/galaxy-integration/jupyterlite/examples/average_col3.ipynb +68 -0
- package/extensions/orbit/vendor/skills/skills/galaxy-integration/jupyterlite/examples/extract_sample_metadata.ipynb +190 -0
- package/extensions/orbit/vendor/skills/skills/galaxy-integration/jupyterlite/examples/variant_annotation.ipynb +816 -0
- package/extensions/orbit/vendor/skills/skills/galaxy-integration/jupyterlite/examples/vcp_variant_map.ipynb +443 -0
- package/extensions/orbit/vendor/skills/skills/galaxy-integration/scripts/README.md +165 -0
- package/extensions/orbit/vendor/skills/skills/galaxy-integration/scripts/galaxy_tool_checker.py +521 -0
- package/extensions/orbit/vendor/skills/skills/galaxy-mcp-reference/SKILL.md +128 -0
- package/extensions/orbit/vendor/skills/skills/galaxy-mcp-reference/gotchas.md +135 -0
- package/extensions/orbit/vendor/skills/skills/galaxy-mcp-reference/history-access.md +132 -0
- package/extensions/orbit/vendor/skills/skills/reproduciblify/SKILL.md +146 -0
- package/extensions/orbit/vendor/skills/skills/reproduciblify/references/directives.yml +496 -0
- package/extensions/orbit/vendor/skills/skills/udt-authoring/SKILL.md +245 -0
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1100
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1101
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1102
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1103
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1104
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1105
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1106
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