TPP:4.5.2 Release Notes

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** Fixed issue of wget not working in Windows (caused by win32_system stripping quotes out of commands -- this is a separate fix) ** Fixed issue of wget not working in Windows (caused by win32_system stripping quotes out of commands -- this is a separate fix)
** Fixed typo in Mascot DB filter box ** Fixed typo in Mascot DB filter box
-* Added check to see if requested scan exists before attempting to perform downstream functions on it.+* [petunia] Add warning if (legacy) mzXML converter is not found on system before attempting to convert, and suggest using msconvert; Move such page to a less prominent place in tab menu; Tone down libraries warning on mscovert page.
* [SpectraST] Option to use the precursor intensity as rank/weight in best-replicate/consensus operation * [SpectraST] Option to use the precursor intensity as rank/weight in best-replicate/consensus operation
* [SpectraST] Follow-up to previous change: In case precursor intensity is not found or is zero, use total ion current instead * [SpectraST] Follow-up to previous change: In case precursor intensity is not found or is zero, use total ion current instead
-* Expanded the RAMP-interface to include id attribute of the spectrum tag in mzML files. The header structure now has char idString[128] 
* [SpectraST] Set fragmentation type to CID by default (instead of leaving it blank) when importing from NIST libraries; allow user to set to others by -cI option * [SpectraST] Set fragmentation type to CID by default (instead of leaving it blank) when importing from NIST libraries; allow user to set to others by -cI option
* [SpectraST] Annotation defaults to CID if unrecognized fragmentation type is encountered. * [SpectraST] Annotation defaults to CID if unrecognized fragmentation type is encountered.
* Overhaul that displays the NSP bin info that no longer uses xslt. * Overhaul that displays the NSP bin info that no longer uses xslt.
-* [petunia] Add warning if (legacy) mzXML converter is not found on system before attempting to convert, and suggest using msconvert; Move such page to a less prominent place in tab menu; Tone down libraries warning on mscovert page.+* Added check to see if requested scan exists before attempting to perform downstream functions on it.
 +* Expanded the RAMP-interface to include id attribute of the spectrum tag in mzML files. The header structure now has char idString[128]
== Bug fixes == == Bug fixes ==

Revision as of 20:02, 6 February 2012

Trans-Proteomic Pipeline (TPP) "Rapture" 4.5.2 Release Notes

Trans-Proteomic Pipeline (TPP) software, release 4.5.2 is a maintenance release that addresses a number of issues found with 4.5.1. 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:4.5.1_Release_Notes Previous release notes are available at TPP:4.5.0_Release_Notes

Contents

New Features

  • Added a utility script to rename Mascot F files to original mz(X)ML base name

Improvements/Changes

  • [petunia] Enhanced Mascot support:
    • Added auto-renaming of Mascot F01234.dat files to original base name of mz(X)ML file
    • Added search info on Mascot results download page
    • Fixed issue of wget not working in Windows (caused by win32_system stripping quotes out of commands -- this is a separate fix)
    • Fixed typo in Mascot DB filter box
  • [petunia] Add warning if (legacy) mzXML converter is not found on system before attempting to convert, and suggest using msconvert; Move such page to a less prominent place in tab menu; Tone down libraries warning on mscovert page.
  • [SpectraST] Option to use the precursor intensity as rank/weight in best-replicate/consensus operation
  • [SpectraST] Follow-up to previous change: In case precursor intensity is not found or is zero, use total ion current instead
  • [SpectraST] Set fragmentation type to CID by default (instead of leaving it blank) when importing from NIST libraries; allow user to set to others by -cI option
  • [SpectraST] Annotation defaults to CID if unrecognized fragmentation type is encountered.
  • Overhaul that displays the NSP bin info that no longer uses xslt.
  • Added check to see if requested scan exists before attempting to perform downstream functions on it.
  • Expanded the RAMP-interface to include id attribute of the spectrum tag in mzML files. The header structure now has char idString[128]

Bug fixes

  • Correct RT model problem present in branch only (fixed in trunk).
  • [SpectraST] Fix obscure bug with option passing; better error checking
  • [SpectraST] Consider all charges when library spectrum has charge 0. This change is already in trunk.
  • [SpectraST] Fix uninitialized value causing wrong Nreps when building best-replicate library
  • [SpectraST] Fix extremely minor memory leak, offending pointer not used anyway
  • [petunia] Install Javascript auxiliary file for table filtering
  • Fixed a memory issue that would cause MzXML2Search to randomly fail
  • [petunia] Minor bugfix to decoy peps and prots processing
  • Adding a quick "hotfix" for users of InSpecT. This fix will install the

latest code changes from Terry Farrah to the program that converts inspect output to pep.xml for use in TPP. This fix is only needed until the developers of inspect release a new version that includes these changes.

  • Correct issue with iProphet probability filtering and naming of columns.


Miscellaneous

  • Nothing to report

Known Issues

  • None to report

Getting the TPP Software

  • Download the TPP version 4.5.2 native windows installer (TPP_Setup_v4_5_RAPTURE_rev_2.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 4.5.2 source code .zip package;

or, check out the code directly from svn: 

 "svn co http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-5-2"

 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:4.5.2_SVN_Log.

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP:4.5.2_Release_Notes"