TPP:4.6.0 Release Notes

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'''Trans-Proteomic Pipeline (TPP) "Occupy" 4.6.0 Release Notes''' '''Trans-Proteomic Pipeline (TPP) "Occupy" 4.6.0 Release Notes'''
- 
----- 
-<span style="color:red">Draft version</span> 
----- 
- 
Trans-Proteomic Pipeline (TPP) software, release 4.6.0 is a minor release of TPP that contains several new features. 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. Trans-Proteomic Pipeline (TPP) software, release 4.6.0 is a minor release of TPP that contains several new features. 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.
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== New Features == == New Features ==
-* ''Support for .mz5 format''+* ''PTMProphet'': new tool for assigning probabilities to PTM-sites
 + 
 +* ''MSGFDB'' support
 + 
 +* Support for ''.mz5'' format
 + 
 +* New ''Petunia'' features:
 +** Support for use of Amazon Web Services, including basic Amazon account management and monitoring
 +** Option to launch ''X!Tandem'' searches on the Amazon cloud (using [[TPP_AMZTPP|amztpp]])
 +** Keep history of launched commands and output; option to delete old output
 +** Launch and monitor multiple commands (don't overwhelm your CPU!)
 +*** New self-updating ''jobs'' page shows all jobs run by user, including old sessions
 +*** Number of ''running'' jobs shows up on window title, updates every few seconds
 +*** Basic monitoring of Amazon cloud jobs
 +** No longer hangs after submitting a job in Windows (self-redirects to ''jobs'' page in 200ms)
 +** Added a button to download a file or a zip archive of files directly from the browser.
 + 
 + 
 +* Add support for ''quick acetyl'' mods from X!Tandem in ''Tandem2XML''
 + 
 +* ''PepXMLViewer'' ions (''ions2'') link goes to ''Lorikeet'' viewer by default; old one is still an option
 + 
 +* Added column in excel ouput of ''protXML viewer'' that indicates if peptide ion is used as evidence
== Improvements/Changes == == Improvements/Changes ==
-* Updated X!Tandem to the latest release: CYCLONE (2011.12.01)+* ''Updated X!Tandem to the latest release: CYCLONE (2011.12.01)''
 + 
 +* Increased the number of threads allowed in X!Tandem from 16 to 256. We don't recommend running 256 threads unless you have a really really big computer.
 + 
 +* Display human readable file sizes in ''Petunia''
== Bug fixes == == Bug fixes ==
-* ''<<insert bulleted new items here>>''+* Various security enhancements
 + 
 +* Fixed bugs associated with ''updateAllPaths.pl''
 + 
 +* Fixed double counting bug (under specific conditions) in ''ProphetModels.pl''
 + 
 +* Fixed bug causing ''XPressPeptideParser'' to run slowly
 + 
 +* ''Petunia'':
 +** Fix bug when converting multiple files to pepXML using semi-cleavage specificity
 +** Specify SpectraST output to have correct '.pep.xml' suffix
 + 
 +* Fixed mzXML output of ''dta2mzxml''
 + 
 +* ''decoyFASTA'' now gracefully deals with empty lines in input fasta file
 + 
 +* Include charge and file downloder perl utilities in Linux ''make install'' step
 + 
 +* ''Lorikeet'':
 +** Do not attempt to populate ms1 data unless we are reading an mz[X]ML file
 +** Fix typos on parameter names for n- and c-terMods
 + 
 +* Added error message to ''mascotout.pl'' if input file not found; also added html footer with TPP version
 + 
 +* Fix webserver accessible file path in ''PepXMLViewer''
== Miscellaneous == == Miscellaneous ==
-* ''<<insert bulleted new items here>>''+* ''No miscellaneous issues to report''
== Known Issues == == Known Issues ==
-* ''<<insert bulleted new items here>>''+* ''No known issues to report''
== Getting the TPP Software == == Getting the TPP Software ==
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For building from source, please refer to the readme file in TPP/src as well as the wiki. 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.+The TPP Team: Luis, David, Mike, Brian, 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 == == SVN Log ==
The SVN log of all changes since the previous release are available at [[TPP:4.6.0_SVN_Log]]. The SVN log of all changes since the previous release are available at [[TPP:4.6.0_SVN_Log]].

Current revision

Trans-Proteomic Pipeline (TPP) "Occupy" 4.6.0 Release Notes

Trans-Proteomic Pipeline (TPP) software, release 4.6.0 is a minor release of TPP that contains several new features. 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:4.5.2_Release_Notes


Contents

New Features

  • PTMProphet: new tool for assigning probabilities to PTM-sites
  • MSGFDB support
  • Support for .mz5 format
  • New Petunia features:
    • Support for use of Amazon Web Services, including basic Amazon account management and monitoring
    • Option to launch X!Tandem searches on the Amazon cloud (using amztpp)
    • Keep history of launched commands and output; option to delete old output
    • Launch and monitor multiple commands (don't overwhelm your CPU!)
      • New self-updating jobs page shows all jobs run by user, including old sessions
      • Number of running jobs shows up on window title, updates every few seconds
      • Basic monitoring of Amazon cloud jobs
    • No longer hangs after submitting a job in Windows (self-redirects to jobs page in 200ms)
    • Added a button to download a file or a zip archive of files directly from the browser.


  • Add support for quick acetyl mods from X!Tandem in Tandem2XML
  • PepXMLViewer ions (ions2) link goes to Lorikeet viewer by default; old one is still an option
  • Added column in excel ouput of protXML viewer that indicates if peptide ion is used as evidence

Improvements/Changes

  • Updated X!Tandem to the latest release: CYCLONE (2011.12.01)
  • Increased the number of threads allowed in X!Tandem from 16 to 256. We don't recommend running 256 threads unless you have a really really big computer.
  • Display human readable file sizes in Petunia

Bug fixes

  • Various security enhancements
  • Fixed bugs associated with updateAllPaths.pl
  • Fixed double counting bug (under specific conditions) in ProphetModels.pl
  • Fixed bug causing XPressPeptideParser to run slowly
  • Petunia:
    • Fix bug when converting multiple files to pepXML using semi-cleavage specificity
    • Specify SpectraST output to have correct '.pep.xml' suffix
  • Fixed mzXML output of dta2mzxml
  • decoyFASTA now gracefully deals with empty lines in input fasta file
  • Include charge and file downloder perl utilities in Linux make install step
  • Lorikeet:
    • Do not attempt to populate ms1 data unless we are reading an mz[X]ML file
    • Fix typos on parameter names for n- and c-terMods
  • Added error message to mascotout.pl if input file not found; also added html footer with TPP version
  • Fix webserver accessible file path in PepXMLViewer

Miscellaneous

  • No miscellaneous issues to report

Known Issues

  • No known issues to report

Getting the TPP Software

  • Download the TPP version 4.6.0 native windows installer (TPP_Setup_v4_6_0.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 4.6.0 source code .zip package;

or, check out the code directly from svn:

 "svn co http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-6-0"
 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, 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:4.6.0_SVN_Log.

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