galaxyproject/loom

Stars: 14
Forks: 12
Open beginner issues: 0
Indexed issues: 117
Avg merge: 6d 5h
Merged PRs (30d): 17

Dominant language: TypeScript
License: MIT
Last GitHub push: Sep 11, 2026
Latest indexed: Sep 16, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

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117 open issues indexed

Loom: /lit command + literature MCPs (PubMed / Europe PMC) Open

galaxyproject/loom#14 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
UX decision log: chat vs. notebook discipline Open

galaxyproject/loom#15 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
UX: confirm scope upfront, not after work is already done Open

galaxyproject/loom#20 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Session bootstrap: present resume/new/review choice instead of auto-continuing Open

galaxyproject/loom#21 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Verify artifacts in Galaxy before claiming completion Open

galaxyproject/loom#23 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Add Anthropic OAuth (Claude Pro/Max) sign-in to Orbit alongside API-key auth Open

galaxyproject/loom#29 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit: configure local/custom models from Preferences UI Open

galaxyproject/loom#30 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Embed CodeBurn cost dashboard in Orbit (per-project, historical, per-model) Open

galaxyproject/loom#32 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit UI review: 6-phase fix plan before alpha release Open

galaxyproject/loom#34 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit: renderer init brittleness — silent module-throw kills app, app.ts monolith, badge HTML lies Open

galaxyproject/loom#36 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Brain prompt: respect local machine capacity when scheduling tools (CPU threads, memory) Open

galaxyproject/loom#61 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit: brain restart doesn't reset renderer UI (badge stuck on "thinking…", Stop button stays visible) Open

galaxyproject/loom#63 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit: stash project context in the Galaxy history so another instance can resume the analysis Open

galaxyproject/loom#69 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit: process monitor goes empty while detached background work is running (nohup/disown reparents out of agent tree) Open

galaxyproject/loom#70 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit: resume-hardening after laptop suspend / long idle (stale Galaxy state, dead-socket tool failures) Open

galaxyproject/loom#72 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit: remote control of local instances via Galaxy as relay (status, prompt, stop from any device) Open

galaxyproject/loom#74 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit: biocontainer-first tool resolution (apptainer) with conda fallback Open

galaxyproject/loom#75 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit: per-session sandbox for agent tool execution (Bubblewrap on Linux/WSL, sandbox-exec on macOS) Open

galaxyproject/loom#76 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit: side-by-side / compare view in the File tab (multiple panes for image+ comparison) Open

galaxyproject/loom#92 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Local job execution via user-installed Pulsar endpoint + relay Open

galaxyproject/loom#97 · 3 comments · 0 reactions · 4 assignees · Indexed Sep 16, 2026
Seamless local-Pulsar setup for user-defined tools (auto-configure from Galaxy preferences) Open

galaxyproject/loom#98 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Right-size always-on system prompt + tool surface for smaller open models Open

galaxyproject/loom#99 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Evaluate Agent SDK credit path for Loom LLM client Open

galaxyproject/loom#110 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Support pi subagents in Loom + Orbit Open

galaxyproject/loom#115 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit: publish analysis directory to GitHub from chat Open

galaxyproject/loom#127 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Per-instance LLM provider/model override via env vars Open

galaxyproject/loom#142 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Electron postinstall silently fails on Linux ARM64 / Node 24 — `npm start` errors with "Electron failed to install correctly" Open

galaxyproject/loom#148 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
[Feature request] Let Galaxy instances host the MCP server so Orbit doesn't need a local `uvx` Open

galaxyproject/loom#149 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Invocation display: step/job counts never populate (completed_steps always 0) Open

bug

galaxyproject/loom#150 · 7 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Initial Orbit impression and Feedback - Jacob Sieg Open

galaxyproject/loom#156 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Context-fill indicator: use Pi's getContextUsage() for an authoritative window % (Option B) Open

galaxyproject/loom#165 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Context-fill indicator flickers (intermittently hidden) during streaming and after model switch Open

galaxyproject/loom#172 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit: `/orbit` v2 -- auto-install Orbit from the release feed when it's missing Open

galaxyproject/loom#178 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Workflow invocation mangles empty/optional parameters (ConnectedValue object stringified into the value) Open

bug

galaxyproject/loom#186 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Agent can't run RNA STARSolo via galaxy_run_tool -- "Parameter 'genomeDir': requires a value, but no legal values defined" Open

bug

galaxyproject/loom#198 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Galaxy MCP: tools return "Not connected" mid-session even though connect reports success (37 tools) Open

bug

galaxyproject/loom#199 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
[Feature request] Auto-discover installed Ollama models via /api/tags instead of a hardcoded list Open

galaxyproject/loom#207 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
galaxy_run_tool can't map a dataset collection over a single-dataset tool input (featureCounts, FastQC) -- "dataset collection supplied to single input dataset parameter" Open

bug

galaxyproject/loom#208 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Galaxy job errors aren't surfaced proactively in Orbit chat -- only when the user asks Open

bug

galaxyproject/loom#210 · 6 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Uploading a large local file via galaxy_upload_file times out (MCP error -32001) and appears to kill the MCP connection Open

bug

galaxyproject/loom#211 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit: provide an async invocation-wait primitive + idle re-nudge (agent blocks on bash `sleep` loops and stalls 30 min–2 h) Open

bug

galaxyproject/loom#215 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit: no PDF-export affordance — runs burn long tails chasing native renderers Open

enhancement

galaxyproject/loom#216 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit: notebook.md exact-string edits fail and force full-notebook rewrites Open

bug

galaxyproject/loom#217 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit: brain assumes a GNU/Linux userland on macOS (`timeout` and other coreutils missing) Open

bug

galaxyproject/loom#218 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit exec-guard denies `curl … | python3` JSON-consume pattern, forcing a brittle temp-file two-step Open

bug

galaxyproject/loom#219 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Brain lacks a cross-assembly gene-ID guardrail — naive locus-tag mapping produced the experiment's only scientific error Open

bug

galaxyproject/loom#220 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Agent reads files outside the project directory without approval, ignoring an explicit "inspect only this directory" instruction Open

bug

galaxyproject/loom#224 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit/Galaxy MCP: no way to browse or import from Galaxy Data Libraries Open

enhancement

galaxyproject/loom#226 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit/Galaxy MCP: no way to save/import a generated .ga workflow into the user's Galaxy Workflows Open

enhancement

galaxyproject/loom#227 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Orbit/Galaxy MCP: no way to delete/purge datasets from a history Open

enhancement

galaxyproject/loom#228 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026

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