omicslab 1.2.0

Python SDK and CLI for the RIVER (OmicsLab) Platform

OmicsLab SDK

Python SDK and CLI for the RIVER (OmicsLab) Platform.

• CLI: omicslab (alias omx) — interact with the platform from your terminal
• Python SDK: omicslab.Client — integrate programmatically

Installation

pip install omicslab

Or from source:

git clone https://github.com/gianglabs/omicslab-platform
cd omicslab-platform/sdk
pip install -e .

Quick Start

1. Authenticate

Create an API token in the web UI (Settings → API Tokens), then:

omicslab auth login --token omx_abc123...

2. Set your context

# Interactive mode — picks org, workspace, and folder
omicslab use

# Or set explicitly
omicslab use --org-id <org_id> --workspace-id <ws_id> --prefix data/

3. Navigate storage like a filesystem

omicslab ls                          # list files
omicslab cd results/                 # change folder
omicslab pwd                         # show current folder
omicslab upload ./data.csv           # upload a file
omicslab download results/output.txt # download a file
omicslab rm old_file.txt             # delete a file
omicslab mv source.txt dest.txt      # move/rename

4. Launch a job

omicslab jobs launch --workspace <ws_id> --analysis <id> --compute <id> --params '{"threads": 8}'
omicslab jobs list --workspace <ws_id>
omicslab jobs logs <job_id> --workspace <ws_id>

CLI Reference

Command group	Description	Examples
auth	Login/logout	omicslab auth login --token ...
token	API token management	create, list, revoke
orgs	Organization CRUD	list, create, get, update, delete, members
ws	Workspace management	list, create, get, update, delete, members
jobs	Launch & manage jobs	launch, list, get, logs, terminate
analysis	Analysis tool catalog	list, create, get, update, delete, pin, schema, tags
studio	Studio tool catalog	list, create, get, update, delete, pin, schema, tags
use	Set active context	Interactive or --org-id, --workspace-id, --prefix
—	File commands	ls, cd, pwd, rm, mv, upload, download, env, whoami

Python SDK

from omicslab import Client

client = Client()  # reads OMICSLAB_TOKEN env or config

# List workspaces
workspaces = client.workspaces.list()

# Launch a job
job = client.jobs.launch_analysis(
    workspace_id="...",
    analysis_id="...",
    compute_id="...",
    params={"threads": 8},
)

# Storage operations
files = client.storage.list("workspace_id", prefix="data/")
url = client.storage.get_upload_url("workspace_id", "data/input.fastq")

Environment Variables

Variable	Purpose
OMICSLAB_TOKEN	API token (overrides config file)
OMICSLAB_BASE_URL	API base URL (default: https://platform.omicslab.io/api)

Configuration is stored at ~/.omicslab/config.json and supports multiple named profiles.