[spctools-discuss] Re: readw MS/MS precursor mass wrong

2009-09-09 Thread Dominik Schwudke
Dear Natalie, sorry for my last email. I had overseen that we have the wrong version again. Thank You again. Natalie Tasman wrote: Hello Dominik, Jimmy, Besides my recommendation to try msconvert, which is the program with more developer focus at this point, there is already a

[spctools-discuss] Re: Problems with TPP installation

2009-09-09 Thread 吕凡
Yes, I have install activeperl 5.8.8.824 and the apache log is following:Installing Apache HTTP 2.0 server with DomainName =cemagref.fr ServerName =xxx.cemagref.fr ServerAdmin = x...@cemagref.fr ServerPort =80 ServerSslPort = 80 ServerRoot =C:/Program Files/Apache Software

[spctools-discuss] TPP 4.3 DB search parameters

2009-09-09 Thread Fil
Hi guys, while upgrading to the 4.3, I'm experiencing some difficulties with the db search process: although selecting any analysis pipeline other than the sequest one (mascot, tandem, spectrast), I always get the Sequest form. Have a nice day Filippo

[spctools-discuss] Re: Problems with TPP installation

2009-09-09 Thread David Shteynberg
Unfortunately this log is not very useful. Perhaps what is needed is the error log. Can you look for any errors towards the bottom of the apache error log that show up after you try to access TPP through your browser? Thanks, -David On Wed, Sep 9, 2009 at 12:24 AM, 吕凡rho...@gmail.com wrote:

[spctools-discuss] Re: OUT2XML generating incorrect XML entry for some out files

2009-09-09 Thread Nikhil Garge
Hello Mr. Eng, Did you get chance to fix the OUT2XML output for SEQUEST outfiles with duplicate_references? Actually the current data I have has few experiments with duplicate refrences options used and hence would be good if an XML file can be created for such experiments. Please let me know.

[spctools-discuss] Re: TPP 4.3 DB search parameters

2009-09-09 Thread Luis Mendoza
Hello Filippo, This is a bug that was introduced in 4.3.0; please check back very soon for the new 4.3.1 release where this is already fixed. In the meantime, you can also fix this issue by a simple edit; just follow the instructions in my reply to this post:

[spctools-discuss] Re: OUT2XML generating incorrect XML entry for some out files

2009-09-09 Thread Jimmy Eng
Thanks for reminding me. I was on vacation when I sent that email last week and forgot all about it. But I'm back and will look into the Out2XML code right now. Assuming (big assumption) I can get it modified today, would you need a Windows binary or are you using the TPP tools on a different

[spctools-discuss] Re: OUT2XML generating incorrect XML entry for some out files

2009-09-09 Thread Nikhil Garge
I am using OUT2XML.exe for our purpose. So Windows binary would be fine. Thanks, ~Nikhil On Wed, Sep 9, 2009 at 1:32 PM, Jimmy Eng jke...@gmail.com wrote: Thanks for reminding me. I was on vacation when I sent that email last week and forgot all about it. But I'm back and will look into

[spctools-discuss] Re: RAW to mzXML (and mzXL) problem TPP4.3

2009-09-09 Thread Oded
Hi , Is it possible to get this bug fix (thanks again Brian) into windows installation package? Thanks, Oded On Aug 17, 9:48 pm, Brian Pratt brian.pr...@insilicos.com wrote: It would be interesting to see the difference between themzXMLfile that worked and the one that didn't. X!Tandem has

[spctools-discuss] new TPP release: 4.3.1 (4.3 revision 1)

2009-09-09 Thread Natalie Tasman
We are proud to offer an update to the Trans-Proteomic Pipeline (TPP) software, release 4.3.1 (4.3 revision 1). The software is available for Windows as well as linux (and unofficially) through osx source from all the usual locations (please see the section below, Getting the software). Most

[spctools-discuss] Re: RAW to mzXML (and mzXL) problem TPP4.3

2009-09-09 Thread Natalie Tasman
Hello Oded, Please see the recently released 4.3.1 version of the TPP, which contains the fix that you mention. Best wishes, Natalie On Sep 9, 2009, at 12:49 PM, Oded wrote: Hi , Is it possible to get this bug fix (thanks again Brian) into windows installation package? Thanks, Oded

[spctools-discuss] Re: RAW to mzXML (and mzXL) problem TPP4.3

2009-09-09 Thread Oded
Thanks Natalie, On Sep 9, 11:57 pm, Natalie Tasman natalie.tas...@insilicos.com wrote: Hello Oded, Please see the recently released 4.3.1 version of the TPP, which   contains the fix that you mention. Best wishes, Natalie On Sep 9, 2009, at 12:49 PM, Oded wrote: Hi , Is it

[spctools-discuss] Re: Problems with TPP installation

2009-09-09 Thread David Shteynberg
What happens when you try to access simply http://localhost ? Thanks, -David On Tue, Sep 8, 2009 at 4:37 AM, rhodearho...@gmail.com wrote: Dear friends, I am installing TPP. Unfortunately, after reboot, the check_env.pl reports as follows: --12:19:49--