Galaxy Server

PittGalaxy installation. To get access, please apply for an allocation. For technical assistance, please post a support ticket.


  1. If you have not already done so, request a user account/allocation on the Center for Simulation and Modeling (SAM) cluster by filling out the required information on this page

  2. If your computer is not connected to the Pitt network (e.g. you are working from home or on a trip), or you are working from a laptop that is connected to the Pitt wireless system, make sure you setup Virtual Private Networking (VPN)(http://core.sam.pitt.edu/offcampusaccess) service, so that you can communicate with the Center for Simulation and Modeling (SAM) cluster.

  3. The Server host is http://galaxy.sam.pitt.edu:8080. Fill in your Pitt username and password. Please note that username is case sensitive and all letters are in lowercase. Refer to the image below for an example of how the settings in this box should look:

     

  4. You can load data from your local computer to galaxy history using the "Get Data > Update File" tool. The limit file size is 2GB. To load larger files or file over 2GB, you can use galaxy data libraries.

     

  5. Running an analysis operates in choosing the tool from left panel and filling in the parameters. The following image shows using the [NGS: RNA Analysis >] Tophat tool to map RNA-seq reads to the dm3 genmome. Every time a tool is run, one or more datasets are created in the user's history.

     

  6. Once you start a job, it will be running on HTC cluster, except the tools under "Get Data", which will be run on galaxy server computer. You will see the status of your jobs on the history.

  7. Vast number of good and well-implemented tools for Galaxy is available through the Galaxy ToolShed. You can submit a SaM help ticket to request installation of them into this Galaxy instance.

  8. Users are assigned default disk quota of 1 TB.

  9. Galaxy data are assigned on /mnt/mobydisk. Note that this /mnt/mobydisk is not backed up, so you will need to be diligent and back up to your own personal data.

  10. If you have any problems with this procedure, please submit a SAM support ticket online (login required)