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

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

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