new TPP release: 4.1.0

[Natalie Tasman]

We are proud to offer a long-awaited major update to the TPP, release 4.1.0.  Releases are available for native windows as well as  linux/osx source from all the usual locations (please see below).

Please note, the converters in the Windows TPP installer are updated, but the standalone releases will follow tomorrow.  Currently, the Agilent .d converter ("trapper") is not yet updated but will be soon.

==Changes in 4.1.0==

[Please note: there are important changes, new features, and bugfixes that are not described in this list.  The developers may add to this list in the future.]

    * Added options to protxml2html to write out HTML or Excel (tab-delimited) from command line;

    * New file downloading tool, fileDownloader.pl, with (optional) md5 verification and unzip;
    * Fixed bug in findsubsets.pl that prevented it from running properly;
    * Added tar (to windows distro);
    * Apache defaults to 5-hour timeout;

    * In Petunia:
          o New page for management (download) of Spectral Libraries;
          o New page to generate Libra condition files - for up to 8 channels (with updated isotopic correction factors);
          o Fixed bug when generating xtandem xml input file;

          o Implemented minimum peptide length option and expanded size of prob. cutoff field for PeptideProphet;
          o Option to pre-run generation of ProteinProphet results in html format;
          o Support for other mzXML converters: mzWiff, massWolf, and trapper (not all options yet);

          o Launch plot-msms when viewing spectra (instead of former dtaviewer);
          o Misc options for MzXML2Search. 

    * Spectrum Viewer updated to automatically select appropriate ion series for display

    * linux build options: many parameters added to Makefile.config.incl (see Makefile.incl)
    * massWolf: thresholding and (experimental) centroiding options
    * ReAdW: calls msconvert for mzML output 

    * TPP's build of X!Tandem now reads mzML, mzXML3, and anything else that the PWIZ library can read.

    * ReadMZXML now reads mzML and anything else that the PWIZ library can read.
    * TPP GUI settings can now be changed by editing tpp_gui_config.pl so your changes to Mascot Server location etc don't get blown away on each software update. 

Download the TPP version 4.1.0 native windows installer
(TPP_Setup_v4_1_JETSTREAM_rev_

0.exe) from the Sashimi SourceForge
project file release page:
http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912

For downloading and installing the (older) Windows cygwin version please visit
the following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"

For downloading the source code, please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"
 or directly from svn: see
http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-1-0
Please refer to the readme file in TPP/src as well as the wiki.

Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/


The SPC Tools Team: Natalie, Luis, and David