TPP:4.7.1 Release Notes

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* iProphet: Fix FPKM message bug. * iProphet: Fix FPKM message bug.
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 +* Sqt2XML: fix bug when empty lines happen in an Sqt, don't quit..skip to next spectrum_query, reported on spctools-discuss
== Miscellaneous == == Miscellaneous ==

Revision as of 17:26, 7 May 2014

***** DRAFT *****

Trans-Proteomic Pipeline (TPP) software, release 4.7.1 is a maintenance release of TPP that contains changes to 4.7.0. The software is available for Windows as well as Linux (and unofficially) through OSX source from all the usual locations (please see the section below, "Getting the software"). Most users are recommended to use the Windows installer, which installs and configures the TPP and other required software (such as a web server). For advanced users who need to customize the TPP, or for those who run high-throughput experiments, you can download the source code. Again, most users don't need build from source, and should use the Windows installer.

Previous release notes are available at TPP:4.7.0_Release_Notes

Contents

New Features

  • CGI/show_tmp_pngfile.pl: added option to keep the png file...show and not delete
  • iProphet: Rewrite spectrum_query index to make unique for quantitation tools.
  • ASAPRatio: Use iProphet probs if present. When running gnuplot test for existence of the png file image before deleting the temporaries.

Improvements/Changes

  • Upgraded Comet to 2014.01 rev. 0
  • Petunia:
    • Made Comet the default search engine; added a link to its project page
    • Removed (rarely used) advanced options for ProteinProphet in xinteract page
    • Added new (default) option of PPM units for AccMass model; also moved this oft-used option to the top
    • Added link to Mayu project page
    • Added 'no spaces' validation for filepaths and other parameters
    • Made sure iProphet page actually catches errors
    • Added warning if speclibs dir does not exist
    • Added option to report probs for decoy hits in PeptideProphet
    • Change 'Paste' button color after click to indicate it is working.
    • Minor formatting and CSS changes
  • PlotSpectraST:
    • Added support for mzML

Bug fixes

  • Fixed the "blank" page presented in Petunia when using basic authentication and you happen to open the main URL without any actions
  • Corrected an issue with Sqt2XML that resulted in a incomplete pep.xml file when the -r option is not used. The -r option now defaults to 10.
  • [X!Tandem] fixed broken modification parsing; suppress warning messages for duplicate mods
  • Corrected an issue when building TPP on linux where the variable PERL_BIN was getting set later in the perl_paths rule, which means ESCAPED_PERL_BIN then is always empty and the resulting TPP didn't know where the perl executable was.
  • PepXMLViewer.cgi: MZRatio is reported as a link only in html mode now, simple value every other mode.
  • iProphet: Fix FPKM message bug.
  • Sqt2XML: fix bug when empty lines happen in an Sqt, don't quit..skip to next spectrum_query, reported on spctools-discuss

Miscellaneous

  • No known issues to report

Known Issues

  • Spectrast (and presumably other TPP programs) have a 2 GB file limit on Windows due to the use of C++ fstreams and the 32-bit libraries they are linked against.

Getting the TPP Software

  • Download the TPP version 4.7.1 native windows installer (TPP_Setup_v4_7_1.exe) from the Sashimi SourceForge project file release page: 
 http://sourceforge.net/projects/sashimi/files/
  • Everyone is encouraged to read and contribute to our wiki, at 
 http://tools.proteomecenter.org/wiki/
  • For guides to installing and using our software, please see our wiki: 
 http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
  • For downloading the source code, please go to the following link: 
 http://sourceforge.net/projects/sashimi/files/ and find the 4.7.1 source code .tgz package;
  • Or, check out the code directly from svn: 
 svn checkout svn://svn.code.sf.net/p/sashimi/code/tags/release_4-7-1
  • For building from source, please refer to the readme file in TPP/src as well as the wiki.

The TPP Team: Luis, David, Mike, Joe, and Jimmy plus all other developers who contributed to this release from the ISB. Thanks to developers and users from the TPP's user community who provided feedback and code contributions.

SVN Log

The SVN log of all changes since the previous release are available at TPP:4.7.1_SVN_Log.

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP:4.7.1_Release_Notes"
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