I gave this a shot, and was able to get through xtandem searching, but when
it came to peptide prophet and xinteract I couldn't get it running. It
seems like xinteract doesn't specify full directories and this causes the
problem.
David
On Monday, March 18, 2013 3:09:05 PM UTC-5, David wrote:
>
> Hello Luis,
>
> I will give this a shot, I didn't see that you replied to this until just
> now. Seems like a good solution. I tried to tear into the source code to
> find this. I'm glad you gave me the line numbers! I'll update you to see
> how it goes shortly.
>
> Thanks again,
> David
>
> On Monday, January 28, 2013 6:41:24 PM UTC-6, Luis wrote:
>>
>> Hello David et.al.
>> You are indeed correct in that Petunia has a built-in mechanism to
>> prevent following symlinks; this is in place so that users do not end up
>> traversing the directory tree to locations where data do not reside or,
>> even worse, to more sensitive parts of the file system.
>> If this is not a large concern for you, you can make a small change to
>> the Petunia code to allow for symlinks. Just edit the line (near line
>> number 714), from:
>> param('workdir', realpath(param('workdir'))."/");
>> to:
>> param('workdir', param('workdir')."/");
>>
>> (mind the parentheses!)
>>
>> I believe this should work, but it will also depend on your exact system
>> configuration.
>>
>> Let me know if you decide to implement this and if it is successful; we
>> may add this as a user-defined option for a future release.
>>
>> Cheers,
>> --Luis
>>
>>
>>
>> On Mon, Jan 28, 2013 at 1:25 PM, David <[email protected]> wrote:
>>
>>> This actually will not work, as by default the tpp_gui.pl script wont
>>> follow symlinks correctly. Ignore previous post.
>>>
>>>
>>> On Monday, January 28, 2013 2:44:24 PM UTC-6, David wrote:
>>>>
>>>> One possible solution is to keep everything in the C: drive, and
>>>> relocate your data drive elsewhere using a hardlink or symlink. I have
>>>> been
>>>> using this with some success in windows 7 and windows 8. I moved my data
>>>> folder to D:/TPP_MS_DATA/ and then I ran an elevated command prompt
>>>> (Administrator) and then ran the command:
>>>>
>>>> mklink /j C:/Inetpub/wwwroot/data/ to D:/TPP_MS_DATA/data
>>>>
>>>> Everything works as expected, all your data is stored somewhere else,
>>>> and you don't have to worry about pathing issues, as even the operating
>>>> system believes that the location of that directory is in
>>>> C:/Inetpub/wwwroot/data/ instead of somewhere else on another drive.
>>>>
>>>> Hope this helps!
>>>>
>>>> Cheers,
>>>>
>>>> David
>>>>
>>>>
>>>> On Friday, November 2, 2012 10:35:34 AM UTC-5, [email protected]:
>>>>>
>>>>> Dear All,
>>>>>
>>>>> This is a "favorite" problem among TPP users, and we thought we had
>>>>> solved it once and for all. But with the new TPP version (4.6.0 and
>>>>> 4.6.1)
>>>>> there are issues with some of the tools when working with data on another
>>>>> drive (G: in our case). I have changed the WEBSERVER_ROOT environment
>>>>> variable, the tpp_gui.pl and of course the httpd.conf to point at G:,
>>>>> and keeping the C:\Inetpub\tpp-bin\ directory. X!Tandem works, but not
>>>>> PeptideProphet or the viewers.
>>>>>
>>>>> Below is our httpd.conf settings and the output from PeptideProphet.
>>>>>
>>>>> Changing everything back to C: makes everything work again, so the TPP
>>>>> installation itself is OK I think.
>>>>>
>>>>> Any ideas?
>>>>>
>>>>>
>>>>> Magnus
>>>>>
>>>>>
>>>>> httpd.conf:
>>>>>
>>>>> #
>>>>> # Begin settings for the Trans Proteomic Pipeline
>>>>> #
>>>>>
>>>>> # Add 24-hour timeout
>>>>> Timeout 86400
>>>>>
>>>>> Alias /tpp-bin "G:/Inetpub/tpp-bin"
>>>>> <Directory "G:/Inetpub/tpp-bin">
>>>>> Options Indexes MultiViews ExecCGI
>>>>> AllowOverride None
>>>>> Order allow,deny
>>>>> Allow from all
>>>>>
>>>>> AddHandler cgi-script .cgi .pl
>>>>> ScriptInterpreterSource Registry
>>>>>
>>>>> PassEnv WEBSERVER_ROOT
>>>>> PassEnv WEBSERVER_TMP
>>>>> </Directory>
>>>>>
>>>>> Alias /ISB "G:/Inetpub/wwwroot/ISB"
>>>>>
>>>>> Alias /schema "G:/Inetpub/wwwroot/schema"
>>>>>
>>>>> <Directory "G:/Inetpub/wwwroot">
>>>>> Options Indexes MultiViews Includes
>>>>> AllowOverride None
>>>>> Order allow,deny
>>>>> Allow from all
>>>>>
>>>>> AddType text/html .shtml
>>>>> AddHandler server-parsed .shtml
>>>>>
>>>>> PassEnv WEBSERVER_ROOT
>>>>> PassEnv WEBSERVER_TMP
>>>>> </Directory>
>>>>> #
>>>>> # End settings for the Trans Proteomic Pipeline
>>>>> #
>>>>>
>>>>>
>>>>> output from PeptideProphet:
>>>>>
>>>>> g:\Inetpub\tpp-bin\xinteract (TPP v4.6 OCCUPY rev 1, Build
>>>>> 201209261035 (MinGW)) running: "C:/Inetpub/tpp-bin/**InteractParser
>>>>> "interact.pep.xml" "121009.LC1.IT1.EC.S0XXXX.**
>>>>> Ecoli_1-B,1_01_3621.tandem.**pep.xml" -L"7"" file 1:
>>>>> 121009.LC1.IT1.EC.S0XXXX.**Ecoli_1-B,1_01_3621.tandem.**pep.xml
>>>>> processed altogether 8922 results results written to file
>>>>> g:/Inetpub/wwwroot/ISB/data/**interact.pep.xml direct your browser to
>>>>> http://localhost/ISB/data/**interact.pep.shtml<http://localhost/ISB/data/interact.pep.shtml>command
>>>>> completed in 2 sec running: "C:/Inetpub/tpp-bin/
>>>>> **DatabaseParser "interact.pep.xml"" command completed in 0 sec
>>>>> running: "C:/Inetpub/tpp-bin/**RefreshParser "interact.pep.xml"
>>>>> "g:/Inetpub/wwwroot/ISB/data/**dbase/18.E_coli_K12.fasta"" -
>>>>> Searching the tree... - Linking duplicate entries... - Printing
>>>>> results...
>>>>> - Building Commentz-Walter keyword tree...command completed in 1 sec
>>>>> running: "C:/Inetpub/tpp-bin/**PeptideProphetParser
>>>>> "interact.pep.xml" MINPROB=0.05" (X! Tandem (k-score)) init with X!
>>>>> Tandem
>>>>> (k-score) trypsin MS Instrument info: Manufacturer: Bruker Daltonics,
>>>>> Model: esquire, Ionization: ESI, Analyzer: Quadrupole Ion Trap, Detector:
>>>>> MS:1000253 PeptideProphet (TPP v4.6 OCCUPY rev 1, Build 201209261035
>>>>> (MinGW)) AKeller@ISB read in 31 1+, 4238 2+, 4472 3+, 0 4+, 0 5+, 0 6+,
>>>>> and
>>>>> 0 7+ spectra. Initialising statistical models ... negmean = -1.1254
>>>>> negmean
>>>>> = -1.74678 negmean = -1.51536 negmean = -0.2 negmean = -0.2 negmean =
>>>>> -0.2
>>>>> negmean = -0.2 Iterations: .........10.........20........**. model
>>>>> complete after 30 iterations command completed in 1 sec running:
>>>>> "C:/Inetpub/tpp-bin/**ProphetModels.pl -i interact.pep.xml" Analyzing
>>>>> interact.pep.xml ... Parsing search results "g:/Inetpub/wwwroot/ISB/data/
>>>>> **121009.LC1.IT1.EC.S0XXXX.**Ecoli_1-B,1_01_3621 (X! Tandem
>>>>> (k-score))"... => Total of 1623 hits. => Total of 0 decoy hits. => Total
>>>>> of
>>>>> 0 excluded hits. command completed in 1 sec running:
>>>>> "G:/Inetpub/wwwroot/../tpp-**bin/PepXMLViewer.cgi -I
>>>>> g:/Inetpub/wwwroot/ISB/data/**interact.pep.xml" This application has
>>>>> requested the Runtime to terminate it in an unusual way. Please contact
>>>>> the
>>>>> application's support team for more information. command
>>>>> "G:/Inetpub/wwwroot/../tpp-**bin/PepXMLViewer.cgi -I
>>>>> g:/Inetpub/wwwroot/ISB/data/**interact.pep.xml" failed: Unknown error
>>>>> command "G:/Inetpub/wwwroot/../tpp-**bin/PepXMLViewer.cgi -I
>>>>> g:/Inetpub/wwwroot/ISB/data/**interact.pep.xml" exited with non-zero
>>>>> exit code: 255 QUIT - the job is incomplete command
>>>>> "g:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -O
>>>>> 121009.LC1.IT1.EC.S0XXXX.**Ecoli_1-B,1_01_3621.tandem.**pep.xml"
>>>>> failed: Unknown error
>>>>>
>>>>> --
>>> 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].
>>> Visit this group at
>>> http://groups.google.com/group/spctools-discuss?hl=en.
>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>
>>>
>>>
>>
>>
--
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 http://groups.google.com/group/spctools-discuss?hl=en.
For more options, visit https://groups.google.com/groups/opt_out.
