usegalaxy.cz

Galaxy is a web-based platform for accessible, reproducible, and transparent computational research. Used by researchers across the globe to access public infrastructure.

Having originated in the bioinformatics community, Galaxy spans numerous scientific disciplines (ecology, chemistry, NLP, climate science, social sciences, …). Nowadays, thousands of computational tools are available, supported by dozens of scientific and software development teams.

The user community is worldwide, with main installations in the US, EU, and Australia, complemented with a network of national installations (usegalaxy.*).

The Czech national service usegalaxy.cz is provided by e-INFRA CZ / MetaCentrum together with ELIXIR CZ.

It provides thousands of tools from various scientific domains and offers large data quotas for Czech researchers and their collaborators.

Accessing usegalaxy.cz

The web interface is available at https://usegalaxy.cz and requires users to log in with either e-INFRA CZ or Life Science login.

• e-INFRA CZ login is available to virtually all Czech academia members via their own institutional credentials. It comes with 250 GB storage space on usegalaxy.cz.
• ELIXIR/Life‑Science is even wider federation of institutions spanning basically the whole Europe and more. It comes with 50GB of storage quota.

User Quotas

Support requests

Please feel free to ask for more resources by emailing galaxy@cesnet.cz.

Describe your project’s needs to us and we will assist with increasing your storage/compute/concurrency or other resource quotas temporarily. We can also install more available tools, help you wrap a new tool for Galaxy, or collaborate on designing a workflow.

Using usegalaxy.cz

The user interface shows:

• list of available tools (left)
• submission form or results of computation (center)
• history, i.e. set of files with their mutual provenance links (right)

The Galaxy Training Network GTN hosts a large collection of tutorials ranging from basic to advanced topics.

• Introduction to Galaxy for beginners:
  • Data import & export – FTP, HTTP, S3, etc.
  • Workflow building – creating, sharing, and publishing pipelines

FTP Upload – Step‑by‑Step

Because Galaxy’s federated log‑ins don’t provide an FTP password out of the box, you need to create one first. Additional steps are required in order to obtain a password for your FTP access:

1. Log in to usegalaxy.cz using one of the federated login options. At this point, you don’t have an FTP password yet.
2. Log out of Galaxy and go to the Galaxy login panel and enter your registered email address into the username field.
3. Click on the Click here to reset your password button.
4. You will receive an email with the reset password link. Check your spam folder if necessary.
5. Click on the provided link and set up a new password for your FTP access.
6. Once you have set a new password, you can use your registered email address and the new password to log in to our ftp server at usegalaxy.cz and copy your files there.
7. Follow the data import process described in the docs.

How to link multiple identities

If you have both e-infra and LSlogin identities you can link them in Galaxy. This prevents problems when switching between log-ins.

1. Click on User in the top menu
2. Select Preferences.
3. Select Manage Third-Party Identities.
4. Choose the other identity provider and authenticate yourself.

References and Use Cases

• Presentation from MetaCenter HPC Seminar 9/2025
• National Repository Platform (NRP) Integration

The following video presentations were delivered during the 2025 EOSC Symposium:

• 4 different Communities (Bio, Astro, Earth, Climate) doing Imaging data analysis in Galaxy
• Earth Science use-case with Volcanoes
• Harmful Algae Blooms in the Baltic Sea analysis
• Social Science and Humanities about land-use plans and OCR