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  1. Registering as a PL-Grid user: please consult the Registration steps section of the user manual (EN) or  Podręcznik użytkownika (PL)
    1. if you are a foreigner, be prepared that you will need your Polish collaborator to confirm your identity - for the PL-Grid operatives to contact the correct person for the confirmation, you will need to obtain the so-called OPI number from that person
    2. alternatively, you may try to look that person up in the Polish science people database (Polish language only, I'm afraid) to obtain the needed OPI number
    3. in case you are a Polish scientist, but you do not have your own OPI number, the one of your supervisor's will suffice
    4. finally, your own OPI  number is enough, if you have one.
  2. Requesting a certificate - again, please follow the user manual (for English version, or Aplikowanie, rejestracja i użycie certyfikatu section in Polish version of the manual) for detailed instruction on how to automatically obtain your own PL-Grid certificate. Here, you will be asked to supply a certificate guard passphrase - please remember what you type as you are going to need it later on.
  3. Requesting access to services; you will need to activate access to two services:
    • " Dostęp do klastra ZEUS " (you will find it inside the "Moje Konto" tab - just click the "Aplikuj o usługę" button)
    • "Diagnostyka molekularna (Galaxy Server)" (the same tab, just slightly below under the "Platforma dziedzinowa: Medycyna Spersonalizowana" section - also click the "Aplikuj o usługę"  button)
  4. Both services should be activated automatically for you, in a couple of minutes, and you will be informed of that fact by an e-mail. Then you are ready to navigate to  https://galaxy.plgrid.pl/  in order to start your first Galaxy session.

  5. The service will use the infrastructure resources grant you have set as your default (it might be your personal resources grant).

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The above are just the most notable toolkits and services integrated into Galaxy, but there are much more (e.g., Cufflinks, (p)BWA, FastQC, Bismark, bedtools, snpEff). In case you need another tool and wrapper available in our Galaxy, just give us a hint at PL-Grid HelpDesk (please, pick the Galaxy queue) and we'll be happy to assist (provided, the license of the tool allows us install it on our resources). What is also important - all these packages are installed on the Zeus computational cluster (the Galaxy server simply shares these packages with Zeus). Hence, in case you would rather use them with traditional command line, you may always log into the Zeus machine (zeus.cyfronet.pl - SSH protocol) and these packages should be available as modules to be loaded. Use the module load command to get access to them.

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Info

In time, we are going to publish more advanced workflows and instructions here. Our NGS experts (Piotr Radkowski, Kacper Żukowski, Marcin Piechota) agreed to deliver some initial content here.

How to Acknowledge PL-Grid Support

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In case you don't have a PL-Grid account yet (so it is not possible to log into the HelpDesk system), or you just want to make it simpler, you may send us an e-mail directly to:   helpdesk@plgrid.pl .

Galaxy Administration

Info

For the time being this section is left empty. However, in time, we are going to provide documentation here will explain what extensions we had to apply to Galaxy sources and to surrounding infrastructure in order to make this work. Responsible for delivering: Łukasz Flis, Maciej Golik and Tomasz Bartyński.

Authors

This Galaxy installation is provided and maintained by ACC Cyfronet AGH and Klaster LifeScience Kraków. The experts from the following institutions provided workflows and tool wrappers for our Galaxy installation:

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