galaxyproject / galaxyproject/brc-analytics

Comparative Genomics Workflow in BRC Analytics

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Description

# First Iteration: Comparative Genomics Tool in BRC Analytics

## Overview

This issue tracks the first iteration of a sequence/assembly comparison tool within BRC Analytics,
modeled after the UCSC prototype:

> **Reference prototype:** https://hgwdev-hiram.gi.ucsc.edu/liftRequest.html

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## Goal

Create a comparison request page within BRC Analytics that mirrors the UCSC prototype interface,
but scoped to assemblies available through BRC Analytics. Submitting the form will trigger the
Galaxy alignment workflow already in development.

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## Entry Point

The tool will be accessible from the BRC Analytics masthead under the heading:

> **"Compare"**

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## User Interface

The page should present a form similar to the UCSC prototype, with the following adaptations:

- **Assembly dropdowns** populated with assemblies available via BRC Analytics (rather than UCSC assemblies).
- A **Submit** button that, once clicked, triggers the Galaxy alignment workflow.

Exact fields and layout should follow the UCSC prototype as closely as practical in the first iteration.

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## Backend: Galaxy Workflow Integration

- On form submission, the selected assemblies and parameters are passed to the existing Galaxy
alignment workflow.
- The workflow is currently available and is being actively refined.
- The BRC page should handle job submission and provide the user with feedback on workflow status
(exact mechanism TBD).

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