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Interface Guide

End-to-End Operating Guide

Command Line and fkit

Results and Reproducibility

Frequently Asked Questions

Platform Agreements and Terms

OpenClaw dual-lane documentation

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Overview

Common Challenges in Bioinformatics Analysis

BioLine- A Standards-Aware, Traceable Analysis Collaborator

End-to-End Experience- From Raw Data to Publishable Results

Reliability Tested Against Published Research

Intended Users

Interface Guide

Project Overview

File

Tool

Flow

Job

Terminal

Setting

AI Section

Quick Start

Create an Account

Create a Project

Prerequisites for First Use

Installation and Environment Validation

Run the Toy Dataset in Five Minutes

Run the First Complete Job

End-to-End Operating Guide

How the Platform Works

Core Concepts

Data Preparation and Input Specifications

BioLine Tool and Flow discovery

Upstream Analysis

Downstream Analysis

Task Execution Lifecycle

Typical Use Cases

Command Line and fkit

Command-Line Architecture

Basic fkit Operations

BioLine Host-Side Scripts

Four-Stage Upstream Lifecycle

Per-Sample Batch Mode

Common Commands

fkit command reference

Sign in — `login`

Upload files or directories — `upload`

List cloud files — `ls`

Move or rename cloud paths — `mv`

Create a cloud directory — `mkdir`

Remove cloud files — `rm`

Copy cloud paths — `cp`

Switch the current project — `project`

Download cloud files — `download`

Create a Tool — `create-tool`

Check and update a Tool — `update`

Pull a Tool version — `pull`

Tool command group — `tool`

Tool configuration commands — `tool config`

Export Tool configuration — `tool config export`

Apply Tool configuration — `tool config apply`

Tool summary commands — `tool summary`

Export Tool summary — `tool summary export`

Apply Tool summary — `tool summary apply`

List Tools — `tool list`

Flow command group — `flow`

Create a Flow — `flow create`

List Flows — `flow list`

Inspect a Flow version — `flow inspect`

File command group — `file`

Search project files — `file search`

Job command group — `job`

Create a Job — `job create`

Read a Job template — `job template`

List Jobs — `job list`

Search Jobs — `job search`

Get Job details — `job get`

Stop a Job — `job stop`

Results and Reproducibility

Result Directory Structure

View Results

Interpret Results

Reproducibility Evidence

Rerun a Historical Job Exactly

Security

Data Boundaries

Container Isolation and Resource Limits

Credential Management

Auditability and Traceability

Frequently Asked Questions

Legacy gateway.sh “Unknown pipeline” Message

Legacy “skill folder missing” Message

A Downstream Tool Task Fails

Failure Caused by Out-of-Memory Conditions

Continue Analysis from an Existing Job

Use a GPU with a Deep-Learning Tool

Files Required Before Analysis

Platform Agreements and Terms

Overview

BioLine Platform Statement

BioLine User Agreement

BioLine Service Terms

BioLine Privacy Statement

BioLine Data Use and Protection

BioLine Supplementary Regulations for Data Protection

OpenClaw dual-lane documentation

Dual-lane architecture

execution registry.yaml

Execution Files, Flows, and Jobs

authoring registry.yaml

Create a Tool

Update a Tool and manage versions

Create a Flow

Legacy downstream image migration inventory

Python/R analysis, plotting, and reports

Failures, document_gap, and quality checks

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