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Galaxy

Galaxy is a web-based platform designed for running computational and statistical analyses with focus on openness and usage of FAIR data. It originally started in biomedical science but nowadays spans numerous scientific domains including ecology, natural language processing, chemistry, climate science, and social sciences.

There is worldwide network of Galaxy servers providing open access to virtually all academic users consisting of "copies" (instances) of the service. Some major ones are hosted in the United States, EU, and Australia. Besides, numerous specialized services exist.

Many quickstart and advanced tutorials are available on Galaxy Training Network.

Metacentrum currently maintains 3 independent Galaxy servers: usegalaxy.cz, RepeatExplorer, and UMSA.

usegalaxy.cz

E-infraCZ / Metacentrum together with Elixir CZ provide the usegalaxy.cz service. It aims at replicating the functionality (set of available tools in particular) of the worldwide services (usegalaxy.org, usegalaxy.eu) while offering significantly higher user quotas (both computational and storage) to the registered CZ users and their collaborators.

Federated Login Options

Metacentrum Galaxy provides two convenient options for logging in:

  1. E-infra AAI which is the prefered way for CZ academic users and it grants higher computing and storage quotas automatically.
  2. Life Science Login If you are associated with the LifeScience/Elixir, you can log in using LifeScience AAI. This is the same method used by usegalaxy.eu and it grants access to the same set of users, with restricted quotas, though.

CZ users, who are able to use E-infra AAI, are able to also log in with Life Science Login in most cases, and they are advised to link them together in Galaxy to avoid future confusion (e.g. not being able to access results stored previously).

The following procedure links the identities:

  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.

User Quotas

The Czech national usegalaxy server at usegalaxy.cz offers 200 GB of free storage quota to users logging in through E-infra AAI or 50GB to the users with Life Science Login. If your research requires more storage please reach us at regalaxy@rt.cesnet.cz with description of your needs.

There is also a limit on the number of jobs a given user can have running concurrently. The usegalaxy.cz instance has this limit set at 10 jobs at the moment. Again, please reach out if this is not sufficient for your needs.

Maximum size of a single dataset is limited at 50 GB.

FTP Access

You can load files into Galaxy using FTP. However due to the nature of federated login additional steps are required in order to obtain 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.

RepeatExplorer

RepeatExplorer is a domain specific Galaxy instance which includes utilities for graph-based clustering and characterization of repetitive sequences in next-generation sequencing data and tools for the detection of transposable element protein coding domains.

We maintain this Galaxy for our partners at Institute of Plant Molecular Biology.

RepeatExplorer Galaxy environment is available at https://repeatexplorer-elixir.cerit-sc.cz/galaxy/.

Registration

  1. Visit registration url
  2. Select account that you will use for registration
    • If you have access to eduIDcz identity (Czech academia) prefer that.
    • Otherwise use Elixir/LS Login or other identity provider from the list
  3. Log in to your selected account and agree when asked to share information with Perun
  4. (optional) if similar user already exists in Perun, you will be asked to prove your identity by logging into this existing account – do this only in case that you want to use this account and it is truly yours (you have to provide correct username and password for this account). If you don’t want to use your already existing account or similar user that Perun found is not you, you can click on the button ”It is not me”.
  5. Please fill the presented application form for Elixir CZ IT services.
  6. Next you will see form to choose username and password for RepeatExplorer Galaxy. If you have chosen to use your already existing account during previous steps these fields will be pre-filled.
  7. Congratulation, you are successfully registered! If you have changed your email address during registration, you will have to verify it. Please check your inbox.
  8. Please expect up to 30m propagation delay before you'll be able to log in to Galaxy.

User Quotas

The RepeatExplorer Galaxy server offers 200 GB of free storage quota to any registered user. If your research requires more storage please reach us at regalaxy@rt.cesnet.cz with description of your needs.

There is also a limit on the number of jobs a given user can have running concurrently. The RepeatExplorer instance has this limit set at 5 jobs at the moment. Again, please reach is if this is not sufficient for your needs.

Maximum size of a single dataset is limited at 250 GB.

FTP Access

RepeatExplorer's FTP server runs at repeatexplorer-elixir.cerit-sc.cz on port 990 and uses the same username and password as RepeatExplorer Galaxy itself.

To learn how to connect to the server and import data to your history please follow the process described in the docs.

Citing RepeatExplorer

Dear users of RepeatExplorer please use the following acknowledgement in your publications using our infrastructure:

Computational resources were provided by the ELIXIR-CZ project (LM2015047), part of the international ELIXIR infrastructure.

Primary Publications

Novak, P., Neumann, P., Macas, J. (2020) – Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2. Nature Protocols 15:3745–3776.

Novak, P., Neumann, P., Pech, J., Steinhaisl, J., Macas, J. (2013) - RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics 29:792-793.

Classification of repetitive elements using REXdb:

Neumann, P., Novak, P., Hostakova, N., Macas, J. (2019) – Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification. Mobile DNA 10:1.

The principle of repeat identification implemented in the RepeatExplorer:

Novak, P., Neumann, P., Macas, J. (2010) - Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics 11:378.

Using TAREAN for satellite repeat detection and characterization:

Novak, P., Robledillo, L.A.,Koblizkova, A., Vrbova, I., Neumann, P., Macas, J. (2017) - TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acid Research 45:e111

Novak, P., Hostakova, N., Neumann, P., Macas, J. (2024) – DANTE and DANTE_LTR: computational pipelines implementing lineage-centered annotation of LTR-retrotransposons in plant genomes. bioRxiv doi: https://doi.org/10.1101/2024.04.17.589915

UMSA

This Galaxy instance provides tools for Untargeted Mass Spectrometry Analysis and we maintain it for our partners at RECETOX.

UMSA Galaxy environment is available at https://galaxy-umsa.grid.cesnet.cz/.

FTP Access

You can load files into this Galaxy using FTP. However due to the nature of federated login additional steps are required in order to obtain password for your FTP access:

  1. Log in to galaxy-umsa.grid.cesnet.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 galaxy-umsa.grid.cesnet.cz and copy your files there.
  7. Follow the data import process described in the docs.

Data Storage Reliability

Data storage of all our Galaxy instances is resilient to normal disk failures and common consistency problems (e.g. power outages). However all users are advised to back up their high-value data elsewhere.

Legacy documentation

Metacentrum used to operate a legacy Galaxy instance till 2023. Its documentation is archived.

Contact & Help

If you need any help or experience tool errors or have unexpected issues with any of the Galaxy instance above please contact us at regalaxy@rt.cesnet.cz.