Furthermore, I also did:
C:\Inetpub\wwwroot\ISB\data\17mixc:\Inetpub\tpp-bin\Tandem2XML
c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tandem
c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tandem.pep.xml
but if I tried to browse file in petunia and click on [PepXML],
I suggest you start debugging the problem one step at a time.
First confirm that your Tandem search actually ran by looking at
contents of the .tandem file.
Next, check contents of tandem.pep.xml.
Do both of these files look like they have peptide IDs in them?
On Wed, Mar 10, 2010 at 2:04 PM,
Hi Jimmy,
Yes, I also checked the .tandem file there were peptides with low expect
score.
I also looked at the .pep.xml file and checked that the scans, hyperscore,
nextscore, bscore, ... matched the .tandem file.
I am puzzled why the run_in doesn't work and wondering if this is affecting
the
I think the fact that run_in doesn't work indicates some kind of system
level problem that's going to make everything else flaky. Perl shouldn't be
an issue, at least at this point.
So c:\inetpub\tpp-bin\run_in c:\; dir doesn't work for you?
What do you see when you type this into your browser
Hi Brian,
On Wed, Mar 10, 2010 at 3:34 PM, Brian Pratt brian.pr...@insilicos.comwrote:
I think the fact that run_in doesn't work indicates some kind of system
level problem that's going to make everything else flaky. Perl shouldn't be
an issue, at least at this point.
So
Did you have a working TPP installation before?
On Wed, Mar 10, 2010 at 3:54 PM, Lik Wee Lee l...@systemsbiology.orgwrote:
Hi Brian,
On Wed, Mar 10, 2010 at 3:34 PM, Brian Pratt
brian.pr...@insilicos.comwrote:
I think the fact that run_in doesn't work indicates some kind of system
level
ah, wait, I do see one weird thing:
WEBSERVER_ROOT = c:\Inetpub\wwwroot;c:\Inetpub\wwwroot
change that environment variable to
WEBSERVER_ROOT = c:\Inetpub\wwwroot
and see how it goes.
On Wed, Mar 10, 2010 at 4:18 PM, Lik Wee Lee l...@systemsbiology.orgwrote:
Nope. I installed it recently
Thanks!!. It is working normally now...phew.
Lik Wee
On Wed, Mar 10, 2010 at 4:46 PM, Brian Pratt brian.pr...@insilicos.comwrote:
It's a windows thing: ControlPanel|System|Advanced|EnvironmentVariables
Good luck!
Brian
On Wed, Mar 10, 2010 at 4:33 PM, Lik Wee Lee
