Hi,
Though I have not tried this on TPP 4.6, but I believe it should work... in
my case I have used wwwroot in different *external SAN *data drive (D) but
note installation of TPP is under C which is default
I can think of the following which you can try and let me know :
a) Make sure you have "tmp" directory under "C" and "G", if it is not there
create it.
b) I have the following Advanced > Environment variables
Under System variable : *Path *: C:\Inetpub\tpp-bin;
Under User variable : *WEBSERVER_ROOT* : D:\Inetpub\wwwroot
c) Though my tpp installation is under C drive (default location), but I
have a copy of tpp-bin under D drive, in your case it should be G.
d) You can copy InetPub folder under your G drive... as is... here is my
structure
D:.
├───tpp-bin
│ ├───images
│ ├───logs
│ ├───Microsoft.VC90.CRT
│ └───users
│ └───guest
└───wwwroot
└───ISB
├───data
│ ├───dataDrive (empty)
│ ├───dbase
│ │ └───speclibs(empty)
│ ├───parameters(empty)
* │ └───SAN =============== THIS IS EXTERNAL DRIVE WHERE ALL DATA
IS WRITTEN*
├───html (as in C drive)
├───schema (contains xsd as in C drive)
e) And here is my httpd.conf
#
# Begin settings for the Trans Proteomic Pipeline
#
# Add 5-hour timeout
Timeout 18000
AddType text/html .shtml
AddHandler server-parsed .shtml
SetEnv WEBSERVER_ROOT D:/Inetpub/wwwroot
SetEnv WEBSERVER_URL http://<yourHost>:<port>
Alias /tpp-bin "C:/Inetpub/tpp-bin"
<Directory "C:/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 "D:/Inetpub/wwwroot/ISB"
Alias /isb "D:/Inetpub/wwwroot/ISB"
<Directory "D:/Inetpub/wwwroot/ISB">
Options Indexes MultiViews Includes ExecCGI
AllowOverride None
Order allow,deny
Allow from all
AddType text/html .shtml
AddHandler server-parsed .shtml
PassEnv WEBSERVER_ROOT
PassEnv WEBSERVER_TMP
</Directory>
On Wed, Mar 20, 2013 at 4:20 PM, David <[email protected]> wrote:
> 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/**InteractPa**rser
>>>>>> "interact.pep.xml" "121009.LC1.IT1.EC.S0XXXX.**Ecol**
>>>>>> i_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/**in**teract.pep.xml direct your browser
>>>>>> to
>>>>>> http://localhost/ISB/data/**inte**ract.pep.shtml<http://localhost/ISB/data/interact.pep.shtml>command
>>>>>> completed in 2 sec running: "C:/Inetpub/tpp-bin/
>>>>>> **DatabasePa**rser "interact.pep.xml"" command completed in 0 sec
>>>>>> running: "C:/Inetpub/tpp-bin/**RefreshPar**ser "interact.pep.xml"
>>>>>> "g:/Inetpub/wwwroot/ISB/data/**d**base/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/**PeptidePro**phetParser
>>>>>> "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/**ProphetMod**els.pl -i interact.pep.xml"
>>>>>> Analyzing interact.pep.xml ... Parsing search results
>>>>>> "g:/Inetpub/wwwroot/ISB/data/**1**21009.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/**in**teract.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/**in**teract.pep.xml" failed: Unknown
>>>>>> error command "G:/Inetpub/wwwroot/../tpp-**bin**/PepXMLViewer.cgi -I
>>>>>> g:/Inetpub/wwwroot/ISB/data/**in**teract.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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