TPP 4.6.1 problems: ions2 / Lorikeet and iProphet (iModelParser.cgi) plots

[Ludovic]

Dear Group, 

I have recently tried to install the TPP4.6.1 in an Ubuntu server system (Ubuntu 10.04.4), following the instructions from the wiki page.

The install seems to have gone fine. All the TPP executable run ok (including the InterProphetParser and PTMprophetParser). 

However, I have 2 problems related to the Petunia viewer:

Problem 1:

By default, it seems that the “ions2” column is now activated to display the MSMS spectra (instead of the “ions” which used to call the plot-msms.cgi).

But this new ions2-Lorikeet spectrum viewer (plot-msms-js.cgi) does not seem to work on my install (I get gray screens in my browser; I tried with Chrome and Firefox). The problem seems to have been reported on the google group, but as far as I know nobody solved it yet:

https://groups.google.com/forum/?hl=en&fromgroups=#!searchin/spctools-discuss/ions2/spctools-discuss/9gx9mxbvews/sat3nZoD1QsJ

 Do you know if I need additional libraries to install the Lorikeet? I tried to install the libjs-jquery-ui library, but it did not help. 

I would not mind using the regular “ions” view, but I don’t know how to change the columns displayed in the Petunia viewer by default?

 

Problem 2:

I also have a problem for displaying the iProphet plots (iModelParser.cgi). I guess this is again a problem with my installation, but I cannot get when it went wrong. The most funny thing is that if you try to open the statistical distribution of a regular interact.pep.xml file with this iModelParser.cgi (by forcing the address/link of the browser instead of the ModelParser.cgi), I actually get plots displayed. But the iModelParser.cgi on an iProphet-interact.pep.xml just opens a white page (tested on Chrome and Firefox). 

Any idea?

 

Thanks in advance for your help.

Best regards

Ludovic

 

[Joseph Slagel]

Ludovic,

The lorikeet problem is a know issue on Linux.  The path to the css/javascript files happen to be hard coded in the source to the directory "/ISB/..." which works only for Windows.  There are two ways to fix it.  The first is by editing the source file src/Visualization/Comet/plot-

msms/plot-msms2.cxx and changing/removing the ISB string.  But the easier solution is to add an alias to your Apache configuration so it can find the files.  So at the bottom of your http.conf file you'll want to add:

Alias /ISB "/proteomics/sw/tpp"

Replacing  the /proteomics/sw/tpp with wherever you have TPP installed.  You'll then need to restart Apache to have the changes take effect.

Also, the original spectrum viewer is still in TPP.  If you want to enable it, in the pepxml viewer click on "pick columns" and add the "ions" column to the list.

-Joe

Ludovic

 

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[Ulrich auf dem Keller]

Hi Ludovic

I also have your 'Problem 2' with iModelParser.cgi on my TPP 4.6.1 installation on Mac OS X 10.8.2. The problem seems to come from the 'pos_obs_dens' and 'neg_obs_dens' attribute values that are dealt with in IModelParser.cxx line 317ff.:

//check if the observed values are present
const char* nObs = tag->getAttributeValue("neg_obs_dens"); //keep in this order, neg obs first in xml
const char* pObs = tag->getAttributeValue("pos_obs_dens");

drawPobs_ = pObs != NULL;
drawNobs_ = nObs != NULL;
next_score->posObs = drawPobs_ ? atof(pObs) : 0;
next_score->negObs = drawNobs_ ? atof(nObs) : 0;

When removing those values from mixturemodel tags in iproph.pep.xml files plots are displayed.

Probably, there is a simple fix for this, and it would be great if a TPP developer could look into it.

Thanks a lot for your help!

Cheers

Ulrich

[Bjorn]

Hi,

I'm installing TPP 4.6.2 on my Mac (10.6.8) and I found that I could not open the ion2 viewer (lorikeet). The suggested solution was to add 

Alias /ISB "/proteomics/sw/tpp" (with "proteomics/sw/tpp" changed to "/usr/local/tpp")

to the apache config file. That modification made it impossible for me to log back into the TPP GUI, so I could not even check if it worked. Can someone assist me with this issue?

Thanks.

Bjorn

[Luis Mendoza]

Hello Bjorn,

If adding the /ISB alias to the Apache configuration does not work, another option is to edit the file:

src/Visualization/Comet/plot-msms/plot-msms-js.cxx .

Find the lines that print the HTML portion of the Javascript tags (lines 107-116 or so) and change the web paths from:

printf(" <script type=\"text/javascript\" src=\"/ISB/html/js/jquery.min.js\"></script>\n");

...to something like:

printf(" <script type=\"text/javascript\" src=\"/tpp/html/js/jquery.min.js\"></script>\n");

...and build again.  Note that this path is the web-accessible path, and not the full system path.

We will try to make this more easily configurable for the next release.

Hope this helps!

--Luis

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[Bjorn]

Great! It worked! Thanks Luis.

Bjorn

[ChargedPeptide]

Hi Bjorn, if you have a working apache config I'd love to see your httpd.conf or virtualhost config, I'm currently beating my head against the wall trying to get CentOS to show spectrums and pep.xml files correctly. While everything else is dandy these two things continue to elude me.
Would be most appreciated.
Erik

[Bjorn]

Hi Erik,

I have no experience with Cent OS, but maybe this can help you:

http://tools.proteomecenter.org/wiki/index.php?title=TPP:Installing_the_Trans-Proteomic_Pipeline_%28TPP%29_4.4.0_on_Mac_OS_X_10.6.4

The page above describes how I installed the TPP on my Mac and contains the changes I made to the the apache2 config file. I hope it also contains the answer to your problems...

Cheers,

Bjorn