Hi Luis, there was a buffer overflow problem with Comet. With help of Jimmy K Eng we could fix it. Now the standard workflow of TPP on MASSyPup is based on Comet as search engine. Both X!Tandem and Comet workflow work fine with a standard data set (included in /tpp/data). On the actual version (today's upload 140528), TPP/Petunia now can be started by a simple "click", directly after starting the Web Browser.
Have fun with the "portable TPP", Robert Am Montag, 19. Mai 2014 09:33:43 UTC-5 schrieb Robert: > > Dear Luis, > > I just uploaded a new release of MASSyPup, with TPP v4.7, Petunia GUI, > X!Tandem workflow and Comet 14.01.rev0 working. > Any comments are welcome. > > Best Regards, > > Robert > > > On 14.05.2014 15:38, Luis Mendoza wrote: > > That's great, Robert! Thanks for including TPP in MASSyPup. > > Does that mean that you are also including the Comet search engine, > since we bundle it with TPP? > Let us know if we can help you iron out those bugs with viewing those > intermediate files. > > Cheers, > --Luis > > > On Sun, Mar 16, 2014 at 6:45 AM, Robert <[email protected]>wrote: > >> Dear colleagues, >> >> the TPP is now portable. The 2014/03/15 release of MASSyPup ( >> http://lababi.bioprocess.org/index.php/lababi-software/78-massypup) >> contains a working Petunia/TPP installation. I tested the >> X!Tandem->PepXML->PeptideProphet->ProteinProphet workflow + viewing. The >> test files are included. >> Both, USB and DVD versions of TPP-MASSyPup, work for me on a 2Gb and a >> 8Gb RAM computer. >> I had to apply plenty of tweaks to get the apache2 running and the custom >> compiled TPP funcional. Some comments: If a Perl script does not work, >> adding '/usr/bin/perl' in the first line usually solves the problem. >> There was no .password file in the release and there is no 'crypt' >> command in Puppy Linux/ Precise Debian. So I disabled the Password check in >> tpp_gui.pl with the comment #RW. Some intermediate .xml files do not >> open, because the interface of the Viewing Utility has some wrong links (a >> '/tpp/' missing in the address), but the important stuff (tandem database >> search, pepXML, Peptide/ProteinProphet, viewing results) works fine. >> If you plan to remaster MASSyPup yourself, you have to copy the following >> files manually from /etc to /tmp/etc during the re-master process: passwd, >> group (I had to edit them manually for adding the www-data user) and the >> apache2 directory (which contains the Apache and TPP configuration). >> Please share your experiences (also pleasant ones) and bug fixes! >> >> Have fun, Robert >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To post to this group, send email to [email protected]. >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
