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 On Wed, Dec 12, 2012 at 1:16 AM, Ludovic <[email protected]> wrote: > 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**** > > ** ** > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/spctools-discuss/-/-XB3yKZpcg4J. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- 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]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
