TPP:4.5.1 Release Notes

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* <del>Fix iProphet models page ("performance" models are missing)</del> * <del>Fix iProphet models page ("performance" models are missing)</del>
-* Fix pepxml2html (view peptide hits) peptide link for SpectraST results+* <del>Fix pepxml2html (view peptide hits) peptide link for SpectraST results</del> ''No longer calling this cgi''
* <del>Petunia: Reindex mzXML: new file with old name; rename old to: old-index</del> * <del>Petunia: Reindex mzXML: new file with old name; rename old to: old-index</del>
* Petunia: option to run xinteract jobs as separate (instead of combining into a single analysis) * Petunia: option to run xinteract jobs as separate (instead of combining into a single analysis)
* <del>Petunia: auto cd to dir and strip out full path if all files in same dir (shorten command line)</del> * <del>Petunia: auto cd to dir and strip out full path if all files in same dir (shorten command line)</del>
-* Petunia: add ETD filter to msconvert+* <del>Petunia: add ETD filter to msconvert</del> ''Seldom-used feature, so suggest using params box''
* <del>iProphet column needs to be renamed (heading for Peptide Prophet Probability and iProphet Probability are both called "probability"</del> * <del>iProphet column needs to be renamed (heading for Peptide Prophet Probability and iProphet Probability are both called "probability"</del>
* <del>Change xinteract to run RefreshParser before PeptideProphet</del> * <del>Change xinteract to run RefreshParser before PeptideProphet</del>

Revision as of 18:48, 7 November 2011

middle
Draft wiki page for the upcoming 4.5.1 release intended only for TPP developers.


Contents

To Do

  • Fix iProphet models page ("performance" models are missing)
  • Fix pepxml2html (view peptide hits) peptide link for SpectraST results No longer calling this cgi
  • Petunia: Reindex mzXML: new file with old name; rename old to: old-index
  • Petunia: option to run xinteract jobs as separate (instead of combining into a single analysis)
  • Petunia: auto cd to dir and strip out full path if all files in same dir (shorten command line)
  • Petunia: add ETD filter to msconvert Seldom-used feature, so suggest using params box
  • iProphet column needs to be renamed (heading for Peptide Prophet Probability and iProphet Probability are both called "probability"
  • Change xinteract to run RefreshParser before PeptideProphet
  • Have InteractParser detect if the search engine is OMSSA and if so apply the fix_pyro_mods_option automatically (do the right thing)
  • Output more significant figs for Protein Prophet weight (rounding error on 0.49 and 0.50)
  • Fix precursor charge column (only 1st letter displayed) and miscalculation of the # of unique peptides in EXCELPEPS
  • Resolve Andreas issue with Tandem2XML
  • Remove potential code injection in show_pepdataset_derivation.pl deferred
  • Remove potential code injection in cometresult.cgi deferred


Trans-Proteomic Pipeline (TPP) "Rapture" 4.5.1 Release Notes

Trans-Proteomic Pipeline (TPP) software, release 4.5.1 is a maintenance release that addresses a number of issues found with 4.5.0. 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 webserver). 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:4.5.0_Release_Notes

New Features

  • Should be none, right? :)

Improvements/Changes

  • Might be a few

Bug fixes

  • Fixed a memory issue in XPressPeptideParser that causes a potential seg fault during runtime.
  • Fixed buffer overrun in mzParser for rare cases where zlib compression increases file size.
  • [Petunia] Fixed an issue were uploading files on Windows resulted in zero byte files.

Miscellaneous

  • Nothing to report

Known Issues

  • None to report

Getting the TPP Software

  • Download the TPP version 4.5.1 native windows installer (TPP_Setup_v4_5_RAPTURE_rev_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 4.5.0 source code .zip package;

or, check out the code directly from svn: 

 "svn co http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-5-0"

 For building from source, please refer to the readme file in TPP/src as well as the wiki.

The TPP Team: Luis, David, Mike, Brian, Natalie, and Joe 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:4.5.1_SVN_Log.

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP:4.5.1_Release_Notes"
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