Great!  Thanks for the update and glad that it works.
--Luis

On Mon, Feb 12, 2018 at 9:48 AM, Volkix <xank...@gmail.com> wrote:

> Hi again,
>
> As Luis suggested it turned out to be a server timeout issue and solved as
> Luis guided. I also installed the ubuntu 16.04 and TPP on it. There is a
> problem with file permissions so petunia cant reach some folders/files. I
> didnt want to spend some more time on it and windows works fine right now.
>
> Thanks again.
> Volkan.
>
> 9 Şubat 2018 Cuma 18:46:58 UTC-5 tarihinde Volkix yazdı:
>
>> Thank you  Luis;
>>
>> For the conf file it seems I have confused so I made some tweaking in the
>> apache conf file. So thank you for warning I will try again for timeout
>> change in that file. I also did the apache restart. As for the linux I
>> tried to install on a linux mint 18 with the instructions on the link you
>> suggested as well. Linux Mint is basically an ubuntu variant. But I will
>> give it another shot by installing ubuntu 16.04. I am more comfortable with
>> linux.
>>
>> Thank you very much again.
>>
>> Volkan.
>>
>> 9 Şubat 2018 Cuma 16:33:06 UTC-5 tarihinde Luis yazdı:
>>>
>>> Hi Volkan,
>>> In Windows you will want to edit this file:  C:\TPP\conf\httpd-tpp.conf
>>> .
>>>
>>> Look for this line, and change the timeout to the desired number of
>>> seconds:
>>>
>>> Timeout *18000*
>>>
>>> Please note that you will need to *restart *the Apache webserver for
>>> any changes to take effect.
>>>
>>> You could also write batch files for Windows.
>>>
>>> As for Linux, which version did you try installing?  We have a page with
>>> updated instructions at:
>>> http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.
>>> 1.0:_Installing_on_Ubuntu_16.04_LTS
>>>
>>> It is worth mentioning that the Linux version of the interface is not
>>> hampered by the webserver timeout.
>>>
>>> Cheers,
>>> --Luis
>>>
>>>
>>>
>>>
>>> On Fri, Feb 9, 2018 at 12:48 PM, Volkix <xan...@gmail.com> wrote:
>>>
>>>> Hi Luis,
>>>>
>>>> I also thought it is a webserver timeout issue. I tried to increase
>>>> that value but didn't work. May be I couldn't put correct things in the
>>>> conf file. Is there any conf file template to avaid server timeout issue.
>>>>
>>>> So I also couldn't install the server on the linux so it is on windows.
>>>> I think I will try to install tpp on linux without petunia and try to work
>>>> with batch scripts.
>>>> Thank you.
>>>> Volkan.
>>>>
>>>> 9 Şubat 2018 Cuma 15:29:52 UTC-5 tarihinde Luis yazdı:
>>>>>
>>>>> Hi Volkan,
>>>>>
>>>>> This may be a webserver timeout issue; how long do the searches run
>>>>> before they seem to stop?
>>>>>
>>>>> The easiest workaround is to simply run in batches of 5-10 files.
>>>>> Another option is to set the webserver timeout to a longer value.  And yet
>>>>> another is to write a script that will do your searches in batch mode,
>>>>> especially if you expect to do this sort of high-volume search regularly.
>>>>>
>>>>> Are you running on Windows or Linux?
>>>>>
>>>>> --Luis
>>>>>
>>>>>
>>>>>
>>>>> On Fri, Feb 9, 2018 at 11:54 AM, Volkix <xan...@gmail.com> wrote:
>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> I have a couple hundreds of raw data to be analyzed. Using the
>>>>>> petunia UI, I convert the files into x(z)ml formats without any problems.
>>>>>> when it comes to X!tandem search analysis goes for 5-15(at most) files 
>>>>>> and
>>>>>> then stops. Petunia says there is a running job however windows task
>>>>>> manager shows no sign of X!tandem as a process. is this a known problem
>>>>>> and/or is there a workaround about this.
>>>>>>
>>>>>> Best
>>>>>> Volkan
>>>>>>
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>>>>>
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