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What is Galaxy?

Photo showing a data analysis running on Galaxy

Galaxy is an open, web-based platform for data intensive biological research that enables researchers to create, run, tune, and share their own bioinformatic analysis.

We will be running training sessions looking at RNA-Seq, ChIP-Seq, Genome Assembly and Variant Calling tools available in Galaxy, and how researchers can build pipelines to process their data.

How to access Galaxy

The Galaxy server is accessed through heighliner.cvr.gla.ac.uk. User creation must be requested by emailing David.McGuinness.2@glasgow.ac.uk. Please include in subject line “GALAXY USER ACTIVATION”. Please feel free to request more than one user activation in a single email. Users MUST be members of the University of Glasgow. User names will be the email address of the person. A password will be set for security reasons however the user MUST set a new one during their first login. This can be done by selecting the “Forgotten password? Reset here” link. The user should shortly receive an email that will allow them to change their password.

Uploading your data

The Galaxy web interface is capable of accepting files up to 2.1GB in size. As a matter of policy, users should instead use the Galaxy FTP server. To connect to the Galaxy FTP, select the FTP protocol, use the address heighliner.cvr.gla.ac.uk as the server, port 21, and your Galaxy username and password as the username and password. The University of Glasgow Galaxy server administrator recommends that users use FileZilla however you may use any FTP client that you are comfortable with.

Data Policy

The Galaxy system is not a data repository and as such, it should never be the only location raw data is stored. You are strictly prohibited from making use of the Galaxy system for the storage or processing of any Personal Data or Sensitive Personal Data as defined by the European Union’s General Data Protection Regulation (GDPR), including but not limited to potentially personally identifying medical data. For more information regarding data protection laws please visit our Galaxy GDPR page. A standard Galaxy user account will be allotted 500GB of space. Once this amount is reached Galaxy will not allow that user to use additional space. Users inactive for more than 38 days will have their data purged. An email will be sent to that user on day 31 with the subject line “Galaxy Data Purge in 7 Days”. If the user then logs in but is again inactive for another week, their data will be purged on the 8th day WITHOUT EMAIL NOTIFICATION.

Galaxy Training

Glasgow Polyomics can provide Galaxy Training. If you or your lab group require training, arrangements can be made. As with all Polyomics Training Courses, these private training courses may carry a cost. If you would like a private Galaxy Training Course please email David.McGuinness.2@glasgow.ac.uk. A request for this kind of training must be submitted 31 days prior to the desired training date.

Tool Installation Requests

Many of the tools used in data intensive research are available as Galaxy tools. If you would like a tool installed on the University of Glasgow Galaxy server, please first check the main Galaxy toolshed found at https://toolshed.g2.bx.psu.edu. If the desired tool exists in the toolshed please send an email to David.McGuinness.2@glasgow.ac.uk with the subject line “TOOL INSTALLATION REQUEST”. The University of Glasgow Galaxy server administrator will then examine the tool to ensure that it is from a reliable source and determine if there will be any issues with it’s implementation. In the event that there is a glut of tool installation requests, a most requested to least requested system will be used to determine which tools get installed first.

In the event that the desired tool does not exist in the main Galaxy toolshed, please send an email to David.McGuinness.2@glasgow.ac.uk with the subject line "TOOL ENQUIRY REQUEST".