TPP:4.7.0 Release Notes

From SPCTools

(Difference between revisions)
Jump to: navigation, search
Revision as of 23:08, 10 February 2014
Dshteynb (Talk | contribs)
(→New Features)
← Previous diff		 Revision as of 23:11, 10 February 2014
Dshteynb (Talk | contribs)
(→Improvements/Changes)
Next diff →
Line 16: Line 16:
* PTMProphet : * PTMProphet :
** support for more modifications ** support for more modifications
 +** improved modification recognition and performance on N-glyco capture data.
* xinteract: * xinteract:
** Allow xinteract to keep running even if -nI is used to disable InteractParser, for using xinteract on previously interacted files (e.g. to do Quantitation separately with xinteract ** Allow xinteract to keep running even if -nI is used to disable InteractParser, for using xinteract on previously interacted files (e.g. to do Quantitation separately with xinteract
 +** If PTMProphet was enabled, xinteract will run quantitation on the PTMProphet results.
* More Descriptive Usage statements * More Descriptive Usage statements
* PeptideProphetParser: * PeptideProphetParser:
** print usage and exit when invoked without arguments. ** print usage and exit when invoked without arguments.
** write directory to inputfile tag when the file path is not absolute, and check for extension...add one if needed. ** write directory to inputfile tag when the file path is not absolute, and check for extension...add one if needed.
 +* InterProphetParser (iProphet):
 +** iProphet: Added optional LENGTH model, and reporting of estimated number of corrects.
 +** KDModel: added more flexibility in bandwidth control.
 +* iModelParser.cgi:
 +** added display of iProphet estimates of total correct PSM and total correct peptides in the results.
* InteractParser: * InteractParser:
** write directory to inputfile tag when the file path is not absolute. ** write directory to inputfile tag when the file path is not absolute.
 +* PepXMLViewer.cgi:
 +** Add start scan back as a sortable column.
 +** Allow iProphet results to link out to the correct search_summary thereby allowing to a link on each spectrum to display the results depending on the best scoring search engine.
== Bug fixes == == Bug fixes ==

Revision as of 23:11, 10 February 2014

Trans-Proteomic Pipeline (TPP) software, release 4.7.0 is a minor release of TPP that contains changes to 4.6.3. 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:4.6.3_Release_Notes

Contents

New Features

  • compareProts_ClusterHM.pl:
    • tool for building heatmaps comparing different ProteinProphet results.
  • ShowXIC.cgi:
    • tool for visualizing Single Ion Current traces.

Improvements/Changes

  • indexmzXML:
    • Allow more upto 100K scans per mzXML file
  • get_prot.pl:
    • filter by probability and any filter out filter_out string
  • PTMProphet :
    • support for more modifications
    • improved modification recognition and performance on N-glyco capture data.
  • xinteract:
    • Allow xinteract to keep running even if -nI is used to disable InteractParser, for using xinteract on previously interacted files (e.g. to do Quantitation separately with xinteract
    • If PTMProphet was enabled, xinteract will run quantitation on the PTMProphet results.
  • More Descriptive Usage statements
  • PeptideProphetParser:
    • print usage and exit when invoked without arguments.
    • write directory to inputfile tag when the file path is not absolute, and check for extension...add one if needed.
  • InterProphetParser (iProphet):
    • iProphet: Added optional LENGTH model, and reporting of estimated number of corrects.
    • KDModel: added more flexibility in bandwidth control.
  • iModelParser.cgi:
    • added display of iProphet estimates of total correct PSM and total correct peptides in the results.
  • InteractParser:
    • write directory to inputfile tag when the file path is not absolute.
  • PepXMLViewer.cgi:
    • Add start scan back as a sortable column.
    • Allow iProphet results to link out to the correct search_summary thereby allowing to a link on each spectrum to display the results depending on the best scoring search engine.

Bug fixes

  • InterProphetParser:
    • BUGFIX with DECOY= option
  • InteractParser:
    • BUGFIX write closing tags when last spectrum query is empty.
  • xinteract:
    • BUGFIX with -MONO option being incorrectly parsed as a PTMProphet command.
    • BUGFIX pep.xml was being appended twice due to typo.

Miscellaneous

  • TBD

Known Issues

  • No known issues to report

Getting the TPP Software

  • Download the TPP version 4.7.0 native windows installer (TPP_Setup_v4_7_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 4.7.0 source code .tgz package;

or, check out the code directly from svn: 

 svn checkout svn://svn.code.sf.net/p/sashimi/code/tags/release_4-7-0
    • For building from source, please refer to the readme file in TPP/src as well as the wiki.

The TPP Team: Luis, David, Mike, 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:4.7.0_SVN_Log.

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP:4.7.0_Release_Notes"
Personal tools