# Building kraken2 + gtdb?

**URL:** https://help.galaxyproject.org/t/building-kraken2-gtdb/16589
**Category:** usegalaxy.org support
**Tags:** reference-index, resources, tool-help, kraken2
**Created:** [December 21, 2025, 8:07pm UTC](https://help.galaxyproject.org/t/building-kraken2-gtdb/16589 "2025-12-21T20:07:12Z")
**Posts on this page:** 1
**Showing post:** 4

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### Author: ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)
#### Post date: [December 23, 2025, 6:45pm UTC](https://help.galaxyproject.org/t/building-kraken2-gtdb/16589/4 "2025-12-23T18:45:13Z")

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Hi @Martyn

The easiest way I can think of – to run this specific job – would be using an account at a public Galaxy server (and our clusters) with a data transfer FTP location. This connects to your local data storage to the public server’s workflows, tools and indexes.

The other choice is to install a Galaxy instance on your cluster, connected to the remote reference data indexes.

## 1. Your remote data storage, with our server, indexes and clusters

We call this type of remote data transfer space a data **Repository**.

### This is where to set it up within an account.

 ![user-pref-manage-repositories-1](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/b/bdf5db19db6044b1ecd8c3761e3ac6a2e364d1e8.png)

### For Step 1 above, click on **Create New** on the first screen to reach this view.

 ![user-pref-manage-repositories-2](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/f/f1a77669e7637789b35978ff786ecefc8e199d82.png)

### Or, you can reach it within the **Upload** tool. This is where you can load data up from the resource into a history.

 ![user-pref-manage-repositories-3](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/8/84ecdaf3617070ce208d5b373510a7e381c944a2.png)

 ![user-pref-manage-repositories-4](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/b/bf55b79308676df772cc644f67edbae128028641.png)

### Then, once you are done, export your history back to your remote location in a compressed archive.

 ![user-pref-manage-repositories-5](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/a/a6147e86f86cae47792c63c3a02e4e21c61cea3a.png)

* * *

## 2. Or, local Docker Galaxy using your cluster, with our remote indexes

**Another choice** could be setting up a simplified local Galaxy server attached to the CVMFS resource. This would have jobs run on your cluster.

The **Docker Galaxy** choice would be quicker to configure and is for exactly use cases like yours – _if you want to use your own cluster_ for the processing.

> [@Private Galaxy Servers](https://help.galaxyproject.org/t/private-galaxy-servers/10861/1):
>
> ### Docker Galaxy
> 
> Much comes pre-configured, and common administrative tasks are simpler to implement and maintain. Be sure to review the repository’s README for these custom instructions.
> 
> 🐋 Docker Galaxy
> 
> - [Galaxy Docker - Galaxy Community Hub](https://galaxyproject.org/use/galaxy-docker/)
> - bgruening/docker-galaxy-stable chat at [https://matrix.to/#/#bgruening\_docker-galaxy-stable:gitter.im](https://matrix.to/#/#bgruening_docker-galaxy-stable:gitter.im)

* * *

So, there are two primary choices if you want to use the Galaxy resources. Please give this a review and let us know what you think or if you have questions! 🛠

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