Thanks for the reply, Joe. I really like the web-interface of not only running TPP but also seeing the PeptideProphet/ProteinProphet results. This will be really helpful for my lab members.
Your second idea is what I am seriously considering. I will definitely look into the scripts in the link. Thanks!! Hyuntae On Jul 6, 12:40 pm, Joseph Slagel <[email protected]> wrote: > Hyuntae, > > You could still install TPP on your account on the supercomputing server -- > just don't install Apache. All of the command line tools will be available > and should still work, you just won't be able to use the Petunia web > interface. In conjunction you could install TPP locally on your desktop. > Then what you could do is copy your data to the cluster to leverage its > usage to run all of your searches and copy the results back to view in > petunia and finish your analysis. Most of the TPP programs should run > easily on a desktop machine on a normal sized data set -- its the searches > that tend to be the most time consuming operation. (If you got really > creative, you could also remotely mount through, say samba, the files from > the linux side to your desktop to be able to view things in petunia. This > is a little complicated to setup and may suffer some performance issues). > > Reading over your cluster resources, I see it supports SGE. You may want to > take a look at a couple of bash shell scripts I put together to run searches > on a cluster. There in our svn repository at: > > http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteom... > > and are meant to be copied and modified as needed. > > -Joe > > > > > > > > On Tue, Jul 5, 2011 at 5:17 PM, Hyuntae <[email protected]> wrote: > > Hi, > > > I am looking into the possibility of installing the whole package of > > TPP in my account at a Linux-based supercomputing server ("Texas > > Advanced Computing Center" see:http://www.tacc.utexas.edu/resources/hpc > > for details), and one of the system administrators said that web- > > servers like Apache are not allowed for installation (mainly due to > > security issues). Does anyone have any suggestions? > > > One of the reasons for considering this server for TPP is to take > > advantage of the speed of searching with parallel computing, so I am > > also thinking of just running the search in the supercomputing server > > and taking care of everything else in TPP installed in a local > > server. But, the speed of transferring big data files (raw data to > > the supercomputing server and search results back to the local server) > > is a sticking issue. > > > Thanks! > > > Hyuntae > > > -- > > You received this message because you are subscribed to the Google Groups > > "spctools-discuss" group. > > To post to this group, send email to [email protected]. > > To unsubscribe from this group, send email to > > [email protected]. > > For more options, visit this group at > >http://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
