Documentationusegalaxy.cz
Galaxy is a web-based solution for handling large scientific datasets, their computational processing, and tracking through the provenance of secondary datasets.
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 mirrors the toolset of the global public instances usegalaxy.org, usegalaxy.eu) with much larger quotas for Czech researchers and their collaborators.
Accessing usegalaxy.cz
Web interface: https://usegalaxy.cz
| Option | Who can use it | How to log in | Typical quota |
|---|---|---|---|
| MetaCentrum account | Anyone with a valid MetaCentrum account (see below) | Use the e-INFRA CZ AAI Login | 200 GB storage, 10 concurrent jobs |
| Life‑Science Login (ELIXIR AAI) | Users registered in the ELIXIR/Life‑Science federated identity system | Click Life Science Login on the Galaxy login page | 50 GB storage, 10 concurrent jobs |
How to obtain a MetaCentrum account
- Go to the MetaCentrum application form
- Sign in via credentials from your institution (Czech academia)
- Follow the instructions
Linking your identities (recommended)
Tip: If you have both identities, link them in Galaxy. This prevents “missing data” problems when switching between log-ins.
- Click on User in the top menu
- Select Preferences.
- Select Manage Third-Party Identities.
- Choose the other identity provider and authenticate yourself.
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
Bookmark the GTN site; most of the tasks you’ll need are already documented there.
User Quotas
| Resource | Limit (standard) | How to request more |
|---|---|---|
| Storage | 200 GB (MetaCentrum / E‑infra AAI) 50 GB (Life‑Science Login) | Send a request to galaxy@cesnet.cz with a short description of your needs. |
| Concurrent jobs | 10 jobs per user (default) | Same e‑mail address – we can raise the limit for large projects. |
| Maximum single dataset | 50 GB | Split large files or ask for a temporary increase. |
If your research requires more storage, please reach out to us at galaxy@cesnet.cz with a description of your needs. All quota changes are evaluated case‑by‑case.
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:
- Log in to usegalaxy.cz using one of the federated login options. At this point, you don’t have an FTP password yet.
- Log out of Galaxy and go to the Galaxy login panel and enter your registered email address into the username field.
- Click on the
Click here to reset your passwordbutton. - You will receive an email with the reset password link. Check your spam folder if necessary.
- Click on the provided link and set up a new password for your FTP access.
- 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.czand copy your files there. - Follow the data import process described in the docs.
Note: The FTP password you set does not affect your Galaxy web login. Keep it safe, but you can reset it at any time via the same password-reset procedure.
Common Tasks at a Glance
| Task | Quick command / UI steps |
|---|---|
| Run a tool | Upload data → Choose a tool from the left panel → Fill parameters → Click “Run” |
| Create a workflow | History → Click the gear ⚙️ → “Create Workflow” → Add steps → Save |
| Share a dataset | Click the dataset’s pencil icon → “Share or Publish” → Add a user’s e‑mail or make the dataset public |
| Check job status | Top‑right History panel shows running/queued/completed jobs; click the i icon for details |
| Request more resources | Email galaxy@cesnet.cz with a short description (quota, compute nodes, etc.) |
| Request another tool | Email galaxy@cesnet.cz with a short description |
| Reset FTP password | Follow steps 2‑4 in the FTP Upload table above |
References and Use Cases
Those video tutorials were given at the EOSC Symposium 2025:
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