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  • Torrent server and Galaxy?

    Hi,
    we are just setting our new PGM up. We currently use Galaxy for a lot of our bioinformatics, run as a local instance on the University high performance computing cluster.
    Does anybody know if it is possible to run a local instance of Galaxy on the Torrent server?

    Cheers,
    Nick

  • #2
    I thought ion torrent end-users did not have access to the torrent server (access being limited through the web interface for the ion software)

    Is your instrument/server set up differently?

    PS: With a web server already running on the torrent server you would need to know your way around system/apache administration to make galaxy work right, if you do have access to the torrent server.

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    • #3
      Thanks for reading & replying.
      I've not looked into it that deeply yet, so it was more of a philosophical question.
      Sounds like installing Galaxy on the Torrent server would be tantamount to jailbreaking the system!
      Our instance of Galaxy currently runs off a different system in another department. The advantage of running it on our torrent server would be that we have supreme oversight of Galaxy and could make changes & upgrades more easily.....

      If i find a way of doing it, i'll make it known.

      Comment


      • #4
        You can ssh to and sudo on the PGM server, so there's no reason you couldn't install Galaxy. It may not be a supported configuration though. Probably easiest if you put everything in your home directory rather than installing system-wide and using an unused port number, so there's less chance of interfering with the Ion environment.

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        • #5
          Thanks Nick, much appreciated.

          Comment


          • #6
            Originally posted by GenoMax View Post
            I thought ion torrent end-users did not have access to the torrent server (access being limited through the web interface for the ion software)

            Is your instrument/server set up differently?

            PS: With a web server already running on the torrent server you would need to know your way around system/apache administration to make galaxy work right, if you do have access to the torrent server.
            You should have full access to your Torrent Server. You can install whatever you like on there, but I would be worried about interfering with the TS software as recently stated.

            Comment


            • #7
              Hi Tucker303,

              recently looked into the same question. In addition to the here stated concerns, the LifeScience rep made it quite clear that you waive your warranty if you install third party software on the IonTorrent server. So especially if you are just starting with the IonTorrent I would consider that carefully.

              Cheers
              Seb

              Comment


              • #8
                Not in our case.

                We are not using the ion torrent machine for production sequencing, so I have not bothered to dig too deeply into this.

                Companies are trying to make these things friendly for bench biologists but they are making life difficult for IT folks by limiting access to these servers. Which in turn means that we are forced to sandbox these servers on our network.

                Originally posted by SeqAA View Post
                You should have full access to your Torrent Server. You can install whatever you like on there, but I would be worried about interfering with the TS software as recently stated.

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                • #9
                  how is your access limited?
                  it's a physical machine with no locked accounts.

                  Comment


                  • #10
                    The only accounts/passwords that we have are for the web interface for ion software.

                    I have not tried to see if the same accounts work via ssh.

                    Originally posted by SeqAA View Post
                    how is your access limited?
                    it's a physical machine with no locked accounts.

                    Comment


                    • #11
                      Physical access; just reboot it in single user mode and set your own root password. Though you probably void your warranty...

                      EDIT: Their brochure says: "Torrent Suite software is offered without warranty of any kind. Linux operating system support is not included in the price of the Torrent Server but separate service contracts are available.". So go ahead and grab the power over your machine.
                      Last edited by arvid; 02-03-2012, 05:39 AM.

                      Comment


                      • #12
                        Let me add the perspective from Ion Torrent directly...

                        First, let me say that we at Ion Torrent have been supportive of the efforts at Galaxy since the start. We are platinum sponsors at their conference this July in Chicago. Register for that here

                        But we cannot recommend trying to run Galaxy on Torrent Server. To be fair, the Torrent Suite software is a careful balance between operating system, database, web service, and a job balancer. When all of this starts getting messed with, then things break. When things break, the data from your PGM doesn't get processed. Work stops. People get angry and it costs money to restore things. Also the probability that data gets lost increases because we have to wipe and restore the server. So warranty or no warranty, hacking your system comes with a risk and a potential financial cost.

                        As an alternative, we keep the Torrent Server fairly open so you can easily get your data off the Torrent Server to whatever platform you'd like. We also have a plug-in infrastructre so you can run a linux executable at the end of your pipeline to handle small jobs (or more ideally - data transfer off the system).

                        Look for Ion Torrent to release Torrent Circuit at the end of Februrary to make it easier for everyone to share these plug-ins through Ion Community and making it easier to install plug-ins through the Torrent Browser. If you want to extend the functionality of your Torrent Server, please consider doing it through a plug-in and then share that with everyone through Torrent Circuit.

                        One last thing, we have been updating Torrent Suite every three month and we have no plans on changing that release schedule. An update will come at the start of April, July, Oct, and Jan. If you hack your system, you can anticipate greater problems during system updates.

                        I just want everyone to know the risks here.

                        Thanks, mike lelivelt - ion torrent
                        Last edited by IonTorrent; 02-04-2012, 02:03 PM.

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