TPP:4.5.0 Release Notes

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-{| style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; border-color: #000; padding: 4px" 
-|[[Image:alert.jpg|middle|left]] 
-|Draft wiki page for the upcoming 4.5.0 release intended only for TPP developers.  
-|} 
-<br> 
- 
'''Trans-Proteomic Pipeline (TPP) "Rapture" 4.5.0 Release Notes''' '''Trans-Proteomic Pipeline (TPP) "Rapture" 4.5.0 Release Notes'''
-Trans-Proteomic Pipeline (TPP) software, release 4.5.0 is a minor release containing new features, new programs, and addresses a number of issues found with 4.4.1. 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.+Trans-Proteomic Pipeline (TPP) software, release 4.5.0 is a minor release containing new features, new programs, and addresses a number of issues found with 4.4.1. 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. As always if you have any questions or problems with this release please let us know on the [http://groups.google.com/group/spctools-discuss spctools-discuss mailing list].
 +''Current release notes are available at [[TPP:4.6.0_Release_Notes]]''<br>
''Previous release notes are available at [[TPP:4.4.1_Release_Notes]]'' ''Previous release notes are available at [[TPP:4.4.1_Release_Notes]]''
== New Features == == New Features ==
 +
 +* New iModelParser.cgi tpp; fpr viewing iProphet models.
 +
 +* New PTMProphetParser tool.
 +
 +* New RTCatalogParser tool for cataloging retention times.
 +
 +* xinteract
 +** New features, report collision energy, report compensation voltage
 +
 +* InteractParser:
 +** New features, report collision energy, report compensation voltage
 +** Adding collision energy and compensation voltage for FAIMS as optional attributes in pepXML schema spectrum_query
 +** SearchHit Changes, also defines bool_hash used in RTCatalog.
 +** Read collision energies in all msms_run_summaries, not just the first one encountered per pepXML file.
 +** Allow InteractParser (or RAMP in general) to read FAIMS Compensation Voltage from mzML filter line. TODO: need to make sure this makes it into the real PWIZ.
 +** New feature precursor intensity in pepXML
 +** Option for recording the retention_time_sec in pepXML.
* Windows installer now allows you to choose which components (such as msconvert) to install. This was done to comply with the licensing requirements of Proteowizard/msconvert. The installer was also streamlined by removing some of the dialog/steps, improving the language of the instructions and changing when certain checks are done as part of the installation process. * Windows installer now allows you to choose which components (such as msconvert) to install. This was done to comply with the licensing requirements of Proteowizard/msconvert. The installer was also streamlined by removing some of the dialog/steps, improving the language of the instructions and changing when certain checks are done as part of the installation process.
 +
 +* New Javascript-based spectrum viewer (Lorikeet)
 +
 +* Petunia:
 +** Added direct access to switch a directory in File Browser
 +** Added user input to pass parameters directly to the command-line (certain executables at this time), including simple validation
== Improvements/Changes == == Improvements/Changes ==
 +* The older ProteoWizard based RAMP mzML/mzXML parse was replaced with mzParser to address some performance problems in a number of different programs.
 +
 +* PepXMLViewer.cgi
 +** Version added to index file so that old index files get regenerated instead of crashing the viewer
 +** Index files now use longs for offsets to support large files
 +** Added collision_energy, precursor_intensity and compensation_voltage support for Crux
 +** Added PTMProphetParser support.
 +
 +* RefreshParser
 +** I->L conversion on peptide and proteins to map to all indistinguishable peptides in the proteins.
 +
 +* ASAPRatio
 +** New options added to quantify only above certain probability.
 +
 +* PeptideProphetParser
 +** tweak pI model to model only +-5 stdev from mean pI for run.
 +** update to correct problem with latest version of Myrimatch which removed some scores in the reports.
 +
 +* XPressPeptideParser
 +** Allow for proper quantitation of combined files where modified masses might be off depending on search engine and use of average vs monoisotopic mass in the search.
 +
 +* RAMP
 +** Adding parsing of compensationVoltage (FAIMS).
 +
 +* iProphet
 +** Clear out tophit hashes before recomputing. Separate SearchHit in a different class.
 +** Remove any peptideprophet or prior interprophet analysis_summary tags.
 +
 +* New pepXML schema update for collision_energy and compensation_voltage
 +
 +* Add scan counters to use as scan numbers when this info is not available in the mzML file (e.g. Agilent QTrap Data)
 +
 +* Fix boost build to work with zlib125's directory structure, delete old zlib123-dll.tar.bz2
 +
 +* Switch to zlib v1.2.5 and tweaks for MingW build
* Rules for fetching Proteowizard and copying msconvert in the Windows installer were added to the Makefile to make builds more automated. * Rules for fetching Proteowizard and copying msconvert in the Windows installer were added to the Makefile to make builds more automated.
 +
 +* Petunia:
 +** Make Tandem the default pipeline;
 +** Added option to run Tandem2XML immediately after searching;
 +** Added support for two missing enzymes in ->pepXML, as well as semi-enzyme support;
 +** Added IPROPHET option to ProteinProphet
 +** Adjusted Xpress defaults;
 +** Centralized code that creates links to open files in respective viewers;
 +** Moved "timeout" link to the right to avoid overlap with update page link;
 +** Added confirmation message when switching pipeline type;
 +** Shortened some menu titles to save space;
 +** Added mouse-over tooltips for menu items and navigation tabs;
 +** Added NIGMS logo and credits; replacing NHLBI's
 +** Took out obsolete SpectraST user options; added decoy-related options and Append To Library feature
 +** Minor formatting fix to PepC page
 +** Small code formatting/alignment changes.
 +** Updated meaning of $in_windows and introduced $in_cygwin vars;
 +** Removed some seemingly unused code.
 +
 +* Protein Sequence Viewer:
 +** Added html comments for easier scrubbing of page (by exporTPP.pl)
 +
 +* Peptide-Protein Weights Viewer:
 +** Fixed page format to fit page width, got rid of wasted space;
 +** Minor HTML tweaks;
 +** Added svn rev;
 +** Code clean-up: took out unused code, re-tabbed/formatted.
== Bug fixes == == Bug fixes ==
-* TBD+* PepXMLViewer
 +** Fixed crash when empty filtered set is returned.
 +** Fixed problem when using commandline generated index which didn't print the queryString so we fake one.
 + 
 +* Tandem2XML
 +** Filter out extension from Tandem spectrum names.
 + 
 +* iModelParser.cgi
 +** Fix bugs with getting page to display. Now displays but the overlapping colors of gnuplot don't work. For best results use gnuplot 4.4.
 + 
 +* InteractParser
 +** Fix Q[111] and E[111] modification reporting in pepXML for OMSSA, max rank option to not report hits above a certain hit_rank.
 + 
 +* iProphet
 +** When the pepXML already contains the iProphet tags filter them out, including the end tag.
 +** Correct the outputting of extra </spectrum_query> tags.
 +** Changes to pepXML writer to correct extra tag issue when iProphet is run on pepXML that already contains iProphet tags.
 + 
 +* Fix parsing of Phenyx search results.
 + 
 +* Petunia:
 +** Minor bug fix when file is not present (as opposed to unreadable).
 +** Fixed broken Set Working Dir feature, also fixed link when output is a directory;
 +** Fixed bug that FileChooser to fail when pressing 'Enter' to switch directory
== Miscellaneous == == Miscellaneous ==
-* TBD+* Nothing to report
== Known Issues == == Known Issues ==
-* None to report+* There is an issue with using the 64bit version of ActiveState's Perl. While the installer recognizes that it is installed all of the Perl programs and scripts are hard-coded to use C:\perl\bin\perl -- the default location for 32bit installations of ActiveState perl. You can either install the 32bit version, or modify all of the scripts to use the 64 bit location (C:\perl64\bin\perl).
== Getting the TPP Software == == Getting the TPP Software ==
-* Download the TPP version 4.5.0 native windows installer (TPP_Setup_v4_5_RAPTURE_rev_1.exe) from the Sashimi SourceForge project file release page:+* Download the TPP version 4.5.0 native windows installer (TPP_Setup_v4_5_RAPTURE_rev_0.exe) from the Sashimi SourceForge project file release page:
"http://sourceforge.net/projects/sashimi/files/" "http://sourceforge.net/projects/sashimi/files/"
Line 54: Line 158:
== SVN Log == == SVN Log ==
-The SVN log of all changes since the previous release are available at [[TPP:4.5.0_SVN_Log#SVN_Log_for_TPP_4.5.0]].+The SVN log of all changes since the previous release are available at [[TPP:4.5.0_SVN_Log]].

Current revision

Trans-Proteomic Pipeline (TPP) "Rapture" 4.5.0 Release Notes

Trans-Proteomic Pipeline (TPP) software, release 4.5.0 is a minor release containing new features, new programs, and addresses a number of issues found with 4.4.1. 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. As always if you have any questions or problems with this release please let us know on the spctools-discuss mailing list.

Current release notes are available at TPP:4.6.0_Release_Notes
Previous release notes are available at TPP:4.4.1_Release_Notes

Contents

[edit]

New Features

  • New iModelParser.cgi tpp; fpr viewing iProphet models.
  • New PTMProphetParser tool.
  • New RTCatalogParser tool for cataloging retention times.
  • xinteract
    • New features, report collision energy, report compensation voltage
  • InteractParser:
    • New features, report collision energy, report compensation voltage
    • Adding collision energy and compensation voltage for FAIMS as optional attributes in pepXML schema spectrum_query
    • SearchHit Changes, also defines bool_hash used in RTCatalog.
    • Read collision energies in all msms_run_summaries, not just the first one encountered per pepXML file.
    • Allow InteractParser (or RAMP in general) to read FAIMS Compensation Voltage from mzML filter line. TODO: need to make sure this makes it into the real PWIZ.
    • New feature precursor intensity in pepXML
    • Option for recording the retention_time_sec in pepXML.
  • Windows installer now allows you to choose which components (such as msconvert) to install. This was done to comply with the licensing requirements of Proteowizard/msconvert. The installer was also streamlined by removing some of the dialog/steps, improving the language of the instructions and changing when certain checks are done as part of the installation process.
  • New Javascript-based spectrum viewer (Lorikeet)
  • Petunia:
    • Added direct access to switch a directory in File Browser
    • Added user input to pass parameters directly to the command-line (certain executables at this time), including simple validation
[edit]

Improvements/Changes

  • The older ProteoWizard based RAMP mzML/mzXML parse was replaced with mzParser to address some performance problems in a number of different programs.
  • PepXMLViewer.cgi
    • Version added to index file so that old index files get regenerated instead of crashing the viewer
    • Index files now use longs for offsets to support large files
    • Added collision_energy, precursor_intensity and compensation_voltage support for Crux
    • Added PTMProphetParser support.
  • RefreshParser
    • I->L conversion on peptide and proteins to map to all indistinguishable peptides in the proteins.
  • ASAPRatio
    • New options added to quantify only above certain probability.
  • PeptideProphetParser
    • tweak pI model to model only +-5 stdev from mean pI for run.
    • update to correct problem with latest version of Myrimatch which removed some scores in the reports.
  • XPressPeptideParser
    • Allow for proper quantitation of combined files where modified masses might be off depending on search engine and use of average vs monoisotopic mass in the search.
  • RAMP
    • Adding parsing of compensationVoltage (FAIMS).
  • iProphet
    • Clear out tophit hashes before recomputing. Separate SearchHit in a different class.
    • Remove any peptideprophet or prior interprophet analysis_summary tags.
  • New pepXML schema update for collision_energy and compensation_voltage
  • Add scan counters to use as scan numbers when this info is not available in the mzML file (e.g. Agilent QTrap Data)
  • Fix boost build to work with zlib125's directory structure, delete old zlib123-dll.tar.bz2
  • Switch to zlib v1.2.5 and tweaks for MingW build
  • Rules for fetching Proteowizard and copying msconvert in the Windows installer were added to the Makefile to make builds more automated.
  • Petunia:
    • Make Tandem the default pipeline;
    • Added option to run Tandem2XML immediately after searching;
    • Added support for two missing enzymes in ->pepXML, as well as semi-enzyme support;
    • Added IPROPHET option to ProteinProphet
    • Adjusted Xpress defaults;
    • Centralized code that creates links to open files in respective viewers;
    • Moved "timeout" link to the right to avoid overlap with update page link;
    • Added confirmation message when switching pipeline type;
    • Shortened some menu titles to save space;
    • Added mouse-over tooltips for menu items and navigation tabs;
    • Added NIGMS logo and credits; replacing NHLBI's
    • Took out obsolete SpectraST user options; added decoy-related options and Append To Library feature
    • Minor formatting fix to PepC page
    • Small code formatting/alignment changes.
    • Updated meaning of $in_windows and introduced $in_cygwin vars;
    • Removed some seemingly unused code.
  • Protein Sequence Viewer:
    • Added html comments for easier scrubbing of page (by exporTPP.pl)
  • Peptide-Protein Weights Viewer:
    • Fixed page format to fit page width, got rid of wasted space;
    • Minor HTML tweaks;
    • Added svn rev;
    • Code clean-up: took out unused code, re-tabbed/formatted.
[edit]

Bug fixes

  • PepXMLViewer
    • Fixed crash when empty filtered set is returned.
    • Fixed problem when using commandline generated index which didn't print the queryString so we fake one.
  • Tandem2XML
    • Filter out extension from Tandem spectrum names.
  • iModelParser.cgi
    • Fix bugs with getting page to display. Now displays but the overlapping colors of gnuplot don't work. For best results use gnuplot 4.4.
  • InteractParser
    • Fix Q[111] and E[111] modification reporting in pepXML for OMSSA, max rank option to not report hits above a certain hit_rank.
  • iProphet
    • When the pepXML already contains the iProphet tags filter them out, including the end tag.
    • Correct the outputting of extra </spectrum_query> tags.
    • Changes to pepXML writer to correct extra tag issue when iProphet is run on pepXML that already contains iProphet tags.
  • Fix parsing of Phenyx search results.
  • Petunia:
    • Minor bug fix when file is not present (as opposed to unreadable).
    • Fixed broken Set Working Dir feature, also fixed link when output is a directory;
    • Fixed bug that FileChooser to fail when pressing 'Enter' to switch directory
[edit]

Miscellaneous

  • Nothing to report
[edit]

Known Issues

  • There is an issue with using the 64bit version of ActiveState's Perl. While the installer recognizes that it is installed all of the Perl programs and scripts are hard-coded to use C:\perl\bin\perl -- the default location for 32bit installations of ActiveState perl. You can either install the 32bit version, or modify all of the scripts to use the 64 bit location (C:\perl64\bin\perl).
[edit]

Getting the TPP Software

  • Download the TPP version 4.5.0 native windows installer (TPP_Setup_v4_5_RAPTURE_rev_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 4.5.0 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.

[edit]

SVN Log

The SVN log of all changes since the previous release are available at TPP:4.5.0_SVN_Log.

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP:4.5.0_Release_Notes"
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