galaxy-cli 1.6.1

Galaxy bioinformatics CLI for automating histories, datasets, tools, workflows, and jobs via the Galaxy REST API

galaxy-cli

galaxy-cli is a compact, machine-readable command-line client for a running Galaxy server. It manages histories, datasets, collections, regular tools, user-defined tools (UDTs), workflows, jobs, and safe recovery of interrupted operations.

The runtime supports Python 3.9–3.13. Server-backed commands require a reachable Galaxy server and API key.

Install

uv tool install galaxy-cli
galaxy-cli --version

Alternatively:

python3 -m pip install galaxy-cli

Configure access

export GALAXY_URL=https://usegalaxy.org
export GALAXY_API_KEY_FILE=secrets/galaxy-api-key
galaxy-cli config test

GALAXY_API_KEY is also supported. Do not put a key in a command, input file, receipt, cache entry, or log. Configuration output masks credentials and the CLI redacts configured keys from stdout, stderr, output files, and errors.

Canonical happy path

galaxy-cli history copy SEED_HISTORY_ID --name analysis
galaxy-cli history find HISTORY_ID --exact-name input.tsv
galaxy-cli tool find "tool name"
galaxy-cli tool inputs TOOL_ID
galaxy-cli tool run TOOL_ID --history HISTORY_ID --inputs @inputs.json
galaxy-cli dataset preview OUTPUT_ID --lines 5

The natural-language names above are aliases. Machine-readable command identity is always normalized to the canonical command:

Alias	Canonical command
tool find	tool search
tool inputs, tool schema	tool template
dataset preview, dataset head	dataset peek
history ls	history list
history find	history resolve
collection get	collection resolve
job debug	job diagnose

All v1.5 canonical names remain valid.

Short structured help

Ask for only the contract needed for one command:

galaxy-cli help tool.run --json
galaxy-cli help dataset.upload --json
galaxy-cli help operation.resume --json

This bounded response contains the canonical command, shortest usage, required values, mechanical defaults, and safety rules. Use tool template only when the exact tool input contract is not already known.

Unified JSON inputs

The recommended form is --inputs @file:

galaxy-cli tool run TOOL_ID --history HISTORY_ID --inputs @inputs.json
galaxy-cli tool validate TOOL_ID --history HISTORY_ID --inputs @inputs.json
galaxy-cli udt run UUID --history HISTORY_ID --inputs @inputs.json

Inline JSON and stdin are also accepted:

galaxy-cli tool run TOOL_ID --history HISTORY_ID --inputs '{"input":{"src":"hda","id":"DATASET_ID"}}'
printf '%s\n' '{"input":{"src":"hda","id":"DATASET_ID"}}' |
  galaxy-cli tool run TOOL_ID --history HISTORY_ID --inputs -

The existing --inputs-json FILE flag remains supported. Do not combine it with --inputs. Inputs must decode to a JSON object; errors never echo the inline payload. Existing -i key=value flags still work and override loaded JSON keys for tool run.

--history is an alias for --history-id.

Blocking results and safe recovery

Tool, UDT, workflow, and upload commands wait by default. One global deadline covers request expansion, every spawned job, and final output metadata. Successful results include final job states and compact dataset/collection metadata, so routine follow-up status calls are unnecessary.

Polling is adaptive by default:

5s, 10s, 20s, 30s, 30s, ...

An explicit --poll-interval N selects the compatible fixed interval.

Mutating operations create secret-free receipts. If a request is interrupted:

galaxy-cli operation resume RECEIPT_ID

In compact results and envelope data, operation_receipt is the receipt ID string itself, not a nested object. Pass it directly to operation show or operation resume. Those commands return the full receipt object.

Resume discovers known requests, jobs, and outputs, waits against one deadline, refreshes final metadata, and never replays an ordinary submission POST. If submission_state is unknown or retry_safe is false, do not resubmit. TUS recovery serializes its one permitted fetch submission with a durable per-receipt lock and rejects a changed local file by size and SHA-256 identity. For a very large source, interruption recovery may require a full file read to finish or revalidate SHA-256; progress is written only to stderr and Ctrl-C cancels the scan. An external receipt path cannot authorize TUS mutation. Use the returned next_commands in envelope/agent mode.

Bounded previews

Head previews use Galaxy's bounded raw-data provider:

galaxy-cli dataset preview DATASET_ID --head 10
galaxy-cli dataset preview DATASET_ID --head 10 --fields 1,3,5 --delimiter tab

--tail and --grep may scan a temporary local copy only when Galaxy reports that the dataset is within the hard 5 MiB preview threshold:

galaxy-cli dataset preview DATASET_ID --tail 10
galaxy-cli dataset preview DATASET_ID --grep 'error|failed' --context 2

Oversized or size-unknown datasets are refused with a suggestion to use an explicit dataset download. Temporary scan files live in the private CLI cache area (or GALAXY_CLI_PREVIEW_TMPDIR), are scanned with bounded streaming selectors, and are removed in a finally path.

Collections require an exact element path:

galaxy-cli collection preview COLLECTION_ID --element sample1/report --lines 5
galaxy-cli tool run TOOL_ID --history HISTORY_ID --inputs @inputs.json \
  --peek-output results --peek-element sample1/report --peek-lines 5

Resolution retains cycle, depth, ambiguity, and result-count guards. The CLI never expands an entire collection or guesses an element.

Stable opt-in output

Default 1.x output remains compact single-line JSON without a new envelope. Opt in when a stable top-level contract is useful:

galaxy-cli --envelope tool run TOOL_ID --history HISTORY_ID --inputs @inputs.json
export GALAXY_CLI_OUTPUT=envelope-v1
galaxy-cli tool run TOOL_ID --history HISTORY_ID --inputs @inputs.json

Envelope v1 has these stable fields:

{
  "schema_version": "1.0",
  "command": "tool.run",
  "success": true,
  "data": {},
  "warnings": [],
  "next_commands": {}
}

--agent enables envelope v1, compact JSON, blocking defaults, bounded lists/strings, a 128 KiB serialized-stdout budget, a 1000-node traversal budget, stderr-only progress, actionable errors, and safe mechanical next commands. Budget exhaustion is reported in warnings. Agent mode never selects a Galaxy tool, changes scientific parameters, rewrites inputs, chooses an output, or executes a next command.

--output-file PATH atomically writes the complete redacted success or error JSON result to the file. Stdout contains only a bounded summary; known API keys are redacted from both the file and the echoed path.

The packaged schema is galaxy_cli/schemas/envelope-v1.json.

Cache observability

Stable read-only server/tool metadata is cached automatically:

galaxy-cli cache stats
galaxy-cli cache clear --namespace tool-schema
galaxy-cli cache warm --server --tools

stats reports namespaces, counts, bytes, fresh/stale/corrupt entries, process-local hit counters, TTL, and hashed server identities. It never returns cached keys or schema bodies. Stored server identities exclude URL credentials, queries, and fragments. Histories, jobs, datasets, operation outputs, UDT results, and scientific data are never warmed.

Set GALAXY_CLI_CACHE_DIR in the launcher to isolate concurrent processes, tasks, or users. Agents normally should not clear or warm caches themselves.

Diagnostics

Errors preserve non-zero exit codes and add mechanical fields such as JSON path, expected type, bounded allowed values, correction, and did_you_mean. Suggestions are never executed.

galaxy-cli job diagnose JOB_ID
galaxy-cli job logs JOB_ID --tail 100 --grep error --context 2

Full execution, safety, cache, and recovery semantics are documented in GALAXY.md. Development and live-test instructions are in galaxy_cli/tests/TEST.md.

Development

uv sync --group dev
.venv/bin/python -m pytest galaxy_cli/tests -q
.venv/bin/ruff check galaxy_cli
.venv/bin/python -m build

Live compatibility tests are explicitly opt-in and use separate usegalaxy/local markers. They never run merely because credentials happen to exist.