Galaxy

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Galaxy installation at UGA

The Galaxy installation at UGA is brought to you by QBCG, IOB and GACRC. The zcluster runs all the jobs submitted to the galaxy system.

The URL to access UGA Galaxy instance is http://galaxy.qbcg.uga.edu this URL might change to a secure one later.

Access to the Galaxy instance is restricted to UGA faculty, staff and students. You will have to be inside UGAs network or signed into the VPN (http://remote.uga.edu) to access the website.

This Galaxy instance requires that you register and login. Registration is open to all UGA related researchers.

Use the following link to register.

If you have any questions, comments or suggestions please contact Raj Ayyampalayam


Loading you data to your galaxy history from your desktop

You have to have a galaxy account before you can upload your data. Once you have your data (reads, reference file etc..) ready you can upload it using ftps (Secure FTP). Your galaxy credentials (username and password) should be used to login to the ftp server at galaxy.qbcg.uga.edu. Make sure that you select explicit TLS encryption in your connection settings. You can use any ftp program(FileZilla, Cyberduck for both you Windows and Mac computers) to upload your data to the import area of Galaxy.

Loading you data stored on zcluster to your galaxy history from your zcluster account

You have to have a galaxy account before you can upload your data. Once you have your data (reads, reference file etc..) ready you can upload it using ftp (regular FTP). Your galaxy credentials (username and password) should be used to login to the ftp server at galaxy.local. You should use the ftp command to upload your data from the zcluster to the import area of Galaxy. It is highly recommended that you use the copy nodes to ftp your files into galaxy.

Example:

raj76@copy1:~$ ftp galaxy.local
Connected to galaxy.local (10.33.31.91).
220-
                *** Welcome to this Galaxy@UGA ftp server! ***

     The current time here is Fri Oct 24 11:49:53 2014.
     If you experience any problems here, contact : raj76@uga.edu


220 ProFTPD 1.3.3g Server (Galaxy@UGA FTP) [10.33.31.91]
Name (galaxy.local:raj76): raj76@uga.edu
331 Password required for raj76@uga.edu
Password:
230 User raj76@uga.edu logged in
Remote system type is UNIX.
Using binary mode to transfer files.
ftp>


List of operational Galaxy tools

This is a list of tools in our Galaxy installation that should be operational. If one of the tools listed here does not work please contact Raj using the comments link above. ---

  1. Fastx toolkit
  2. NGS: QC and manipulation
    • The Illumina read tools should all work
    • Need to test other sequencing technology
  3. Tophat2 and Cufflink tools all work
    • You have to run your data (reads) via "fasta groomer" tool
  4. Trinity denovo RNA-Seq assembler

Screen shots

Here are some screen shots of CyberDuck and Filezilla configuration:

Galaxy-FTPS-CyberDuck.png

Galaxy-FTPS-FileZilla.png