I think its working now. I guess I just needed to restart the computer. I think it had something to do with reinstalling a different version of perl for SEQUEST, setting the paths for the correct version of perl for TPP, and restarting the computer.
I'll let you know if I have any more issues. Thanks, Kris On Aug 31, 6:58 pm, Brian Pratt <[email protected]> wrote: > Looks like a path issue - the run_in command is normally found in > c:\Inetpub\tpp-bin . > > On Mon, Aug 31, 2009 at 2:59 PM, Kris <[email protected]> wrote: > > > I like the idea of using junction points. But for some reason it's > > still not working. I installed TPP on the C: drive, and I made a > > junction point for the SEQUEST location and a junction point for the > > data folder. > > > Now, I'm getting errors when I run a database search. > > > E.G.: > > * c:/Inetpub/wwwroot/ISB/data/PAe000163_test_9-1-09/005a.pep.xml > > [ Unreadable! ] > > * c:/Inetpub/wwwroot/ISB/data/PAe000163_test_9-1-09/005b.pep.xml > > [ Unreadable! ] > > * c:/Inetpub/wwwroot/ISB/data/PAe000163_test_9-1-09/005c.pep.xml > > [ Unreadable! ] > > * c:/Inetpub/wwwroot/ISB/data/PAe000163_test_9-1-09/020a.pep.xml > > [ Unreadable! ] > > * c:/Inetpub/wwwroot/ISB/data/PAe000163_test_9-1-09/020b.pep.xml > > [ Unreadable! ] > > * c:/Inetpub/wwwroot/ISB/data/PAe000163_test_9-1-09/020c.pep.xml > > [ Unreadable! ] > > * c:/Inetpub/wwwroot/ISB/data/PAe000163_test_9-1-09/060a.pep.xml > > [ Unreadable! ] > > * c:/Inetpub/wwwroot/ISB/data/PAe000163_test_9-1-09/060b.pep.xml > > [ Unreadable! ] > > * c:/Inetpub/wwwroot/ISB/data/PAe000163_test_9-1-09/060c.pep.xml > > [ Unreadable! ] > > * c:/Inetpub/wwwroot/ISB/data/PAe000163_test_9-1-09/900a.pep.xml > > [ Unreadable! ] > > * c:/Inetpub/wwwroot/ISB/data/PAe000163_test_9-1-09/900b.pep.xml > > [ Unreadable! ] > > * c:/Inetpub/wwwroot/ISB/data/PAe000163_test_9-1-09/900c.pep.xml > > [ Unreadable! ] > > > run_in c:/Inetpub/wwwroot/ISB/data/PAe000163_test_9-1-09; c:\Inetpub > > \tpp-bin\runsearch -pc:/Inetpub/wwwroot/ISB/data/PAe000163_test_9-1-09/ > > sequest.params -P15 005a.mzXML > > > 'run_in' is not recognized as an internal or external command, > > operable program or batch file. > > > Command FAILED > > > Command 2 [Mon Aug 31 17:56:16 2009] [ Show / Hide ] > > > run_in c:/Inetpub/wwwroot/ISB/data/PAe000163_test_9-1-09; c:\Inetpub > > \tpp-bin\runsearch -pc:/Inetpub/wwwroot/ISB/data/PAe000163_test_9-1-09/ > > sequest.params -P15 005b.mzXML > > > 'run_in' is not recognized as an internal or external command, > > operable program or batch file. > > > Command FAILED. > > > -Kris > > > On Aug 24, 1:07 pm, "Brian Pratt" <[email protected]> wrote: > > > You can compile that with gcc and mingw. But: > > > > You might prefer to have a go with symbolic links (junction points, in > > > windows-world): > > > >http://en.wikipedia.org/wiki/NTFS_junction_point > > > > as discussed in a different thread today: > > > >http://groups.google.com/group/spctools-discuss/msg/f8a5637d11bddb15?... > > > > The idea would be to create a directory c:\xcalibur that is just a > > pointer > > > to d:\xcalibur > > > > Good luck! > > > > Brian > > > > -----Original Message----- > > > From: [email protected] > > > > [mailto:[email protected]] On Behalf Of Kris > > > Sent: Sunday, August 23, 2009 4:28 PM > > > To: spctools-discuss > > > Subject: [spctools-discuss] Re: specify the location of sequest > > > > I can't seem to get microsoft visual studios 2005 professional > > > edition. Is there any other software I could possibly use to compile > > > the software? Or could I even just have someone else compile it for me > > > and send me what I need? > > > > Thanks, > > > Kris > > > > On Aug 7, 2:55 pm, Jimmy Eng <[email protected]> wrote: > > > > Unfortunately you'll need to edit and recompile runsearch1.c (around > > > > line 165) which is in the TPP's src/util/ directory. Follow up here if > > > > that's something you need assistance with. > > > > > Kris wrote: > > > > > Hi everyone, > > > > > > I've searched the forums, but I can't seem to find where you specify > > > > > the path for SEQUEST. > > > > > > When I run a database search, I get the following error: Cannot find > > > > > Sequest executable in c:\xcalibur\system\programs\bioworksbrowser\ > > > > > > I have everything installed on the D drive of my computer. I think I > > > > > have everything configured correctly except for the location of > > > > > SEQUEST. SEQUEST is located at d:\xcalibur\system\programs > > > > > \bioworksbrowser\. Which file do I have to modify to set the sequest > > > > > path to my D: drive? > > > > > > Thanks, > > > > > Kris --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
