I reran and Fixed it I think. Sorry about all the posts.
On Friday, December 2, 2016 at 9:41:17 AM UTC-5, Kevin Hart wrote:
>
> Actually..... im now getting this error
> ------------------------------
> *0 total peptides, 0 unique stripped peptides*
> Legacy Viewer worked on one sample. If I look at ProtXML I have lots of
> peptides so im not sure why im getting this error.
> On Friday, December 2, 2016 at 9:04:33 AM UTC-5, Kevin Hart wrote:
>>
>> I reinstalled TPP 5.0 in the correct directory and legacy viewer is now
>> working. Thank you for working through all of this with me
>>
>> On Wednesday, November 30, 2016 at 5:07:41 PM UTC-5, Luis wrote:
>>>
>>> Hi Kevin,
>>> Do you have 2 versions of TPP installed concurrently on the same
>>> machine? It looks like the installation of 5.0 was done with "C:\TPP\"
>>> specified as the data directory; but you are using data in the previous TPP
>>> data directory "C:\Inetpub\wwwroot\ISB\" .
>>>
>>>
>>> One quick way to get this fixed and allow you to use the legacy viewer
>>> is the following:
>>>
>>> 1. Open the file C:\TPP\cgi-bin\protxml2html.pl -- in Notepad or your
>>> favorite text editor.
>>>
>>> 2. Scroll down to around line 44, just *after *the line that says use
>>> tpplib_perl; # exported TPP lib function points
>>>
>>> 3. Add the following *new *line:
>>> *$ENV{'WEBSERVER_ROOT'} = 'C:/Inetpub/wwwroot/ISB/';*
>>>
>>> 4. Save this file.
>>>
>>> 5. Finally, if the following file exists, delete it* (please match the
>>> file ending carefully!!)
>>> C:/Inetpub/wwwroot/ISB/data5.0/SEL55/SEL55.Comet.Tandem.interact.prot.
>>> *xsl*
>>>
>>> * You should likewise delete any other existing .xsl files if you find any
>>> trouble opening its corresponding prot.xml file
>>>
>>>
>>> You should now be able to use the legacy viewer with any file that is
>>> located in this data area. Do note that this is a bit of a temporary fix,
>>> and I recommend that you reinstall TPP 5.0 with the correct settings at a
>>> future date, or when/if you update to the next version, once we release it.
>>>
>>> Hope this helps!
>>>
>>> --Luis
>>>
>>>
>>> On Wed, Nov 30, 2016 at 10:55 AM, Kevin Hart <[email protected]>
>>> wrote:
>>>
>>>> Gladly. On our machines were not getting an error it just simply will
>>>> not generate a page. The page is completely blank. Attached are both files
>>>> so you can take a look.
>>>>
>>>> On Tuesday, November 29, 2016 at 4:34:50 PM UTC-5, Luis wrote:
>>>>>
>>>>> The new viewer has been updated to display and export protein length.
>>>>> It will be included in the next release of TPP, but I'd be glad to
>>>>> forward
>>>>> you an advance copy so that you can get to your data.
>>>>>
>>>>> And I have not been able to see what's wrong with the legacy viewer; I
>>>>> just tested it in 3 different machines and seems to be working. Can you
>>>>> share your protXML file so I can try to debug? Furthermore, if there is
>>>>> a
>>>>> problem with the code, an error might have been logged to the web server
>>>>> error log; you can explore this by opening the file httpd-error.log,
>>>>> typically found under C:\TPP\log\ . Or if you don't mind sharing this
>>>>> file, I can have a look.
>>>>>
>>>>> Cheers,
>>>>> --Luis
>>>>>
>>>>>
>>>>> On Tue, Nov 29, 2016 at 5:20 AM, Kevin Hart <[email protected]>
>>>>> wrote:
>>>>>
>>>>>> Do you know how to get it to export protein length with the .tsv file
>>>>>> from ProtXML?
>>>>>>
>>>>>>
>>>>>> On Wednesday, November 23, 2016 at 3:52:08 PM UTC-5, Kevin Hart wrote:
>>>>>>>
>>>>>>> I can see both tables and graphical models. My files were not where
>>>>>>> TPP thought they were and thus confusion arose when I clicked on models
>>>>>>> in
>>>>>>> ProtXML. ProtXML just didnt know where to look.
>>>>>>>
>>>>>>> Legacy Viewer was nice because I was able to select different things
>>>>>>> to be displayed like protein length and all of those other toggles. I
>>>>>>> cant
>>>>>>> find a way in ProtXML to have it export those other things for me so I
>>>>>>> can
>>>>>>> generate SAF and NSAF values.
>>>>>>>
>>>>>>> On Wednesday, November 23, 2016 at 1:26:24 PM UTC-5, Luis wrote:
>>>>>>>>
>>>>>>>> That's great. Can you only see the tables? Or also the graphical
>>>>>>>> models?
>>>>>>>>
>>>>>>>> The legacy viewer is being phased out in favor of the new one, and
>>>>>>>> is slated for removal from distribution. Is there a specific function
>>>>>>>> that
>>>>>>>> you need from it that the new one does not have?
>>>>>>>> If you really need it soon, you could install a previous version of
>>>>>>>> TPP on a different computer and open your file there.
>>>>>>>>
>>>>>>>> --Luis
>>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, Nov 23, 2016 at 9:10 AM, Kevin Hart <[email protected]>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> I am able to gain access now to the error sensitivity tables but
>>>>>>>>> still need access to legacy viewer.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Monday, November 21, 2016 at 11:42:45 AM UTC-5, Kevin Hart
>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>> I downloaded and am using the new version of TPP(5.0) on Windows
>>>>>>>>>> 7 however im running into a small issue. I can not access the
>>>>>>>>>> error/sensitivity tables through both ProtXML Viewer (Forbidden You
>>>>>>>>>> don't
>>>>>>>>>> have permission to access
>>>>>>>>>> /tpp/data/SEL42/SEL42.Tandem.Comet.interact.prot-MODELS.html on this
>>>>>>>>>> server.) and legacy viewer is not loading at all. Unfortunately I
>>>>>>>>>> need
>>>>>>>>>> these things to run all of my analysis. If anyone would have a work
>>>>>>>>>> around
>>>>>>>>>> or fix for this I would appreciate it.
>>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> You received this message because you are subscribed to the Google
>>>>>>>>> Groups "spctools-discuss" group.
>>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
>>>>>>>>> send an email to [email protected].
>>>>>>>>> To post to this group, send email to [email protected].
>>>>>>>>> Visit this group at
>>>>>>>>> https://groups.google.com/group/spctools-discuss.
>>>>>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>> You received this message because you are subscribed to the Google
>>>>>> Groups "spctools-discuss" group.
>>>>>> To unsubscribe from this group and stop receiving emails from it,
>>>>>> send an email to [email protected].
>>>>>> To post to this group, send email to [email protected].
>>>>>> Visit this group at https://groups.google.com/group/spctools-discuss.
>>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>>
>>>>>
>>>>> --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "spctools-discuss" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to [email protected].
>>>> To post to this group, send email to [email protected].
>>>> Visit this group at https://groups.google.com/group/spctools-discuss.
>>>> For more options, visit https://groups.google.com/d/optout.
>>>>
>>>
>>>
--
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to [email protected].
To post to this group, send email to [email protected].
Visit this group at https://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/d/optout.
