Re: [spctools-discuss] Re: binaries not found via Petunia

That's good to hear. I should have known that petunia is using hard coded paths. That's not to say somewhere else buried deep in TPP there might be some problems. -Joe On Wed, Feb 29, 2012 at 12:54 PM, Brian Hampton wrote: > Hi Joe, > > I just removed the "export PATH=$PATH:/usr/local" from a

[spctools-discuss] Re: binaries not found via Petunia

Hi Joe, I just removed the "export PATH=$PATH:/usr/local" from apache2/ envvars, restarted apache2 and petunia works fine. So it was the tpp_gui_config.pl error I made that caused the problem. Thanks, Brian On Feb 29, 2:19 pm, Joseph Slagel wrote: > Brian, > > I think your PATH environment var

[spctools-discuss] Re: binaries not found via Petunia

Hi Joe, I went down numerous envar PATHs with no success. However, I think it turned out to be my mistake when editing the first install tpp_gui_config.pl file I put the paths in the wrong place: THIS DOESN'T WORK: # # SET ENVIRONMENT VARIABLES HERE 'base_dir' => '/usr/local/tpp/', 'www_root

Re: [spctools-discuss] GLYC not working in 4.5.2?

I see the modification N[115], but not the color coding and also the calculation at the bottom of the page for # NxS/T peptides vs total # peptides is empty. I find this to be very useful when calculating specificity of our capturing method. If i know it is a bug, then I'll wait for a fix. Just wan

[spctools-discuss] Re: binaries not found via Petunia Ubuntu 10.10 install

I got Petunia to work after reading Based on the SPCTools Wiki for installing tpp in Ubuntu 10.04.3 called for installing in /usr/local/tpp. I have seen many posts where tpp is installed in /usr/local/apps/

[spctools-discuss] OMSSA and X!Tandem with different mods

OMSSA takes considerably longer than X!Tandem to search when searching for multiple modifications (mainly due to X!Tandem's use of "refinement" mode.) Therefore, we'd like to do the modification searches using X!Tandem and leave OMSSA to just do "normal" searches (ie only 1 modification, that of ox

[spctools-discuss] OMSSA -hl parameter and PeptideProphet/iProphet/ProteinProphet

Hi, We're running OMSSA, but it turns out that performance is significantly improved if we use a smaller value for the -hl option. (That is, instead of the default of 30, we'd like to set it to say 5, eg -hl 5). Because the hl is defined as follows: -hl maximum number of hits retained per p

Re: [spctools-discuss] binaries not found via Petunia

Brian, I think your PATH environment variable isn't including the TPP bin directory. You could try adding it to envvars like so and restarting Apache: echo "PATH=$PATH:/usr/local/tpp/bin:" | tee -a /etc/apache2/envvars If this solves you problem please let me know and I'll update the instructio

[spctools-discuss] Re: Attempt to access forbidden directory TPP-4.5.1 build 201201261618

So which is better to do, change the specification in the tpp_gui.pl from: my $data_dir    = readconfig('data_dir',"${www_root}ISB/ > data/");           # full path to data directory top-level to: my $data_dir    = readconfig('data_dir',"${www_root}/ > data/");           # full path to data di

[spctools-discuss] binaries not found via Petunia

Hello, I have installed TPP 4.5.2 on Ubuntu 10.10 using the instructions here In those instructions there are a couple of errors where chown is used when the command should be chmod. However, I believ

Re: [spctools-discuss] 2 libra questions

Rich, Since no one else has responded, I'm staring at iTRAQ data I just processed through Libra today and the intensities reported in the pepXML file are exactly those that are in the corresponding mzXML. I have never seen data where this is not the case which means something went wrong somewhere

Re: [spctools-discuss] GLYC not working in 4.5.2?

Hello Ruby, I believe this problem is only with the ProteinProphet viewer not the modelling. Someone else had reported this problem also but it has not been fixed in this release. The problem is in the coloring off the motif only. You should still see the motif in the peptides you identify.

[spctools-discuss] GLYC not working in 4.5.2?

I have been using the GLYC command in TPP 4.4.0 for more than a year with no problem. I recently upgraded to TPP 4.5.2 and can't seem to get the GLYC command to work for ProteinProphet. I have the "N- glycosylation data (color NXS/T)" option checked in petunia when doing ProteinProphet processing,