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]
> <javascript:>>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
>>>>
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