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 <javascript:>> 
> 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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