Using different data drive (wwwroot) in TPP 4.6.X

[Magnus....@gmail.com]

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 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

[Brian Hampton]

Hi Magnus,

This is one job I want to tackle at some point but haven't the time yet.  Mostly because Tandem runs so much faster on Ubuntu than Win7.  But I have difficulties getting a fully functioning Pipeline on linux.  So I use Win7 for all the post search analysis.  I use a series of SED commands to remap the embedded directory paths for use on the Wiin7 box.  Thanks for posting your config file.  It will help me when the time comes.

Have a look at (assuming you are using Tandem) the contents of the .tandem search result file and the input file specific tandem.params files in a browser window or text editor and note the directory paths in there.  Does it say:  G:.... or C:....

The path written in the result file comes from the location of the input files e.g. .mzXML file and locations of the params and database used for the search.  My guess is the problem is the embedded directory paths in the search result are not G:... but are C:... and the Pipeline can't find the files because they are looking in G:... as per your config files.  This would indicate your setup is the problem.  Just a guess but is a place to start.

Good luck,

Brian

Brian Hampton
Protein Analysis Lab
Center for Vascular and Inflammatory Diseases
University of Maryland School of Medicine
800 West Baltimore Street Rm 307
Baltimore  MD  21201
V: 410-706-8207
F: 410-706-8234

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[David]

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

[David]

This actually will not work, as by default the tpp_gui.pl script wont follow symlinks correctly. Ignore previous post.

[Luis Mendoza]

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

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[David]

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

[David]

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

[Vishal Swaroop]

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>

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