# Troubleshooting the Kraken2 Data Manager and CVMFS indes

**URL:** <https://help.galaxyproject.org/t/troubleshooting-the-kraken2-data-manager-and-cvmfs-indes/16256>\
**Category:** Uncategorized\
**Tags:** devops-administration, data-manager, galaxy-docker\
**Created:** [September 13, 2025, 4:30am UTC](https://help.galaxyproject.org/t/troubleshooting-the-kraken2-data-manager-and-cvmfs-indes/16256 "2025-09-13T04:30:49Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Chetan\_Mahale](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/chetan_mahale/32/7485_2.png) [@Chetan\_Mahale](https://help.galaxyproject.org/u/Chetan_Mahale)\
**Post date:** [September 13, 2025, 4:30am UTC](https://help.galaxyproject.org/t/troubleshooting-the-kraken2-data-manager-and-cvmfs-indes/16256/1 "2025-09-13T04:30:49Z")

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Hi All, I wanted to install Galaxy server on my local hosting using ubuntu server. I wanted to scan the fungi data files for its classification. Can any one please provide a script which can do the galaxy installation and required data set download task ?

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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:** [September 15, 2025, 10:53pm UTC](https://help.galaxyproject.org/t/troubleshooting-the-kraken2-data-manager-and-cvmfs-indes/16256/2 "2025-09-15T22:53:12Z")

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Welcome @Chetan_Mahale

If this is a new Galaxy server, you should consider using the Docker Galaxy version. It will be much easier to set up and most of this will be done for you already. If this interests you, start here:

> [@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)

* * *

For an existing Galaxy server, you have two choices:

Install the Kraken2, then the Data Manager, and configure it to run on your server.

- Linked to the Tool Shed for the tool → [Galaxy | Tool Shed](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_build_kraken2_database/201eff2131d6)
- The Development repository (as a reference since it includes an example) → [galaxytools/data\_managers/data\_manager\_build\_kraken2\_database at master · dfornika/galaxytools · GitHub](https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database)

Or, you can use our CVMFS resource to get these same database indexes. This would allow you to use any of the pre-built indexes we host at servers like [UseGalaxy.org](http://UseGalaxy.org) (for this tool, and most of the others!).

See [the tool form here](https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy2) to review what is available for Kraken2. These databases will correspond to the source indexes hosted at → [Index zone by BenLangmead](https://benlangmead.github.io/aws-indexes/k2) (where you can access the source data directly).

Both methods are covered in our administrative tutorials.

- **Data Management & Reference Data** → [Galaxy Server administration / Tutorial List](https://training.galaxyproject.org/training-material/topics/admin/)
- More administrative resources → [Private Galaxy Servers](https://help.galaxyproject.org/t/private-galaxy-servers/10861)

Please give those a review and let us know if you have any follow up questions! 🙂

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<div class="post-metadata">

**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:** [March 17, 2026, 4:25am UTC](https://help.galaxyproject.org/t/troubleshooting-the-kraken2-data-manager-and-cvmfs-indes/16256/3 "2026-03-17T04:25:27Z")

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