TPP:4.8.0 Release Notes
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| - | <span style="color:red">'''*** THIS IS A DRAFT DOCUMENT FOR DEVELOPERS ONLY ***'''</span> | + | Trans-Proteomic Pipeline (TPP) software, release 4.8.0 is a minor release of TPP that contains new features, improvements, and fixes to 4.7.1. The software is available for Windows as well as Linux (and unofficially) for OSX 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 on Linux or OS X, 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 4.8.0 is a minor release of TPP that contains new feaures, improvements, and fixes to 4.7.1. 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 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:4.7.1_Release_Notes]]'' | ''Previous release notes are available at [[TPP:4.7.1_Release_Notes]]'' | ||
| Line 7: | Line 5: | ||
| == New Features == | == New Features == | ||
| - | * ProteinProphet: GROUPWTS used by default now and OCCAMS razor is now sharper than with GROUPWTS before this change. For old GROUPWTS behavior use SOFTOCCAM option. NOGROUPWTS added for original behavior without GROUPWTS used. Also added count of distinct peptide sequences. | + | * ''ProteinProphet:'' GROUPWTS used by default now and OCCAMS razor is now sharper than with GROUPWTS before this change. For old GROUPWTS behavior use SOFTOCCAM option. NOGROUPWTS added for original behavior without GROUPWTS used. Also added count of distinct peptide sequences. |
| - | * ProteoGrapher | + | * ProteoGrapher: new tool for visualizing ProteinProphet prot.xml files in the context of Gene Ontology terms |
| + | * ''Petunia:'' | ||
| + | ** Added page for ''idconvert'' (under new ''Files'' section) | ||
| + | ** Added page for ''reSpect'' (under ''Utilities'') | ||
| + | ** Added page for running DNA to AA 6-frame translation utility | ||
| + | ** Added drop-down for quick file select; points to dbase/ and speclibs where appropriate | ||
| + | ** Point to new ProtXMLViewer as default; leave link to legacy viewer | ||
| + | ** Allow search results to be written in directory other than where mz[X]ML files are: | ||
| + | *** Comet and X!Tandem: use location of respective params file | ||
| + | *** SpectraST: added input field for output dir (-sO option in SpaectraST) | ||
| + | * ''tpp_models:'' | ||
| + | ** Support for charting ASAPRatio pvalue data and model | ||
| + | ** Display ASAP mean ratio in linear (as well as default log) | ||
| + | ** Added ability to highlight NSP bin and display peptide values alongside NSP table | ||
| + | ** Added support for FPKM model info and Libra parameters | ||
| + | * The version string now contains Subversion revision information generated by the program [http://svnbook.red-bean.com/en/1.7/svn.ref.svnversion.re.html svnversion]. | ||
| == Improvements/Changes == | == Improvements/Changes == | ||
| + | * Comet: updated to version 2014.02 rev. 2 | ||
| * PTMProphet: L[119] modification | * PTMProphet: L[119] modification | ||
| * plotspectrast.cgi: set GNUPLOT_BINARY definition at build time | * plotspectrast.cgi: set GNUPLOT_BINARY definition at build time | ||
| * Respect: cleanup some code, default minprob 0.5 | * Respect: cleanup some code, default minprob 0.5 | ||
| * SpectraST: Peptide new mod for DiMethyl-C13HD2 | * SpectraST: Peptide new mod for DiMethyl-C13HD2 | ||
| + | * ''ASAPRatio:'' | ||
| + | ** Enable wavelet option | ||
| + | ** Write pvalue raw data and model into protXML file | ||
| + | ** Lowered bin size on pvalue modeling from 0.05 to 0.02 (to get finer-grained model and values) | ||
| + | * ''xinteract:'' | ||
| + | ** Run tpp_models.pl on all relevant files after the tmp directory shenanigans have taken place | ||
| + | ** Got rid of suppoprt for ancient (perl) ProteinProphet | ||
| + | ** Got rid of calls to extinct peptide and protein viewers | ||
| + | ** Cleaned up usage statement | ||
| + | ** Reformatted code to have consistent indentation; Other minor code cleanup | ||
| + | * ''Petunia'' | ||
| + | ** Made dir listing '''much''' faster (by removing calls to extremely inefficient tpplib_perl for file extension checking) | ||
| + | ** Broke out file browsing link (''Files'') to new section; moved updatePaths to this section | ||
| + | ** Tool access menu items now span the entire row, with orange hover color | ||
| + | ** Increased alpha opacity for menus | ||
| + | ** Added 'dir_exists' validation | ||
| + | ** Highlight (red color) the words 'warning' and 'error' when viewing command output | ||
| + | ** Link bare .dta files to Lorikeet viewer | ||
| + | ** Added new MS3 (Thermo) option to Libra | ||
| + | ** Added link to ProteoGrapher for .prot.json files | ||
| + | ** Added option to run ProteinProphet from iProphet page | ||
| + | ** Test for amztpp prior to letting users enter their credentials | ||
| + | ** Catch "ParserDetails.ini" line from amztpp when expecting an XML-only response | ||
| + | ** Add error message as mouse-over when amz log-in fails | ||
| + | ** Use '&' to separate commands in windows, move towards stripping out run_in | ||
| + | * ''ProtXMLViewer:'' | ||
| + | ** Added NSP bin link (goes to models page, with extra URL params) | ||
| + | ** Added charge state to peptide link to PepXMLViewer (to get better set of related spectra) | ||
| + | ** Implemented generic support for Libra (removed hard-coded channel masses and related code) | ||
| + | ** Added ability to sort by Libra channel | ||
| + | ** Added distinction between 'n/a' quant ratios vs 'no result' (all peptides rejected) | ||
| + | ** Added hard-coded secondary sort (by probability, or npeps) | ||
| + | ** Changed 'peptides' to 'PSMs' in column heading | ||
| + | ** Added support for Gaggle and JSON output -- and link to new ''ProteoGraphic'' tool | ||
| + | ** Added basic command-line support | ||
| + | ** Added 'single sequence entries' statistic | ||
| + | ** Added option to display all peptides in single page (like old viewer) | ||
| + | ** Warn user when no results passed filtering criteria | ||
| + | ** Capture protein length | ||
| + | ** Change cursor to 'wait' when loading data | ||
| + | ** Minor formatting and css updates | ||
| + | * ''PepXMLViewer:'' | ||
| + | ** Link PeptideProphet probability to new models page | ||
| + | ** Auto run tpp_models if models page does not exist | ||
| + | ** Remove link to more_pepanal.pl; replace with direct link to static html models page | ||
| + | ** Replace hard-to-read ptm_peptide field (which had in-line probs for each potential AA) with a graphical bar-chart of probs above the peptide sequence -- with mouse-over site probs | ||
| + | ** Highlight modified AAs in ptm peptide string | ||
| + | |||
| == Bug fixes == | == Bug fixes == | ||
| - | * RespectParser: Use stat to check for file's existence instead of try catch block that was crashing on windows. | + | * ''RespectParser:'' |
| - | * RespectParser: report each spectrum only once per file. | + | ** Use stat to check for file's existence instead of try catch block that was crashing on windows. |
| - | * InteractParser: remove errorneous path from spectrum name when occurring | + | ** report each spectrum only once per file. |
| - | * InteractParser: BUGFIX When the MS datafile not read in successfully don't try to access the spectrumList or it crashes. | + | ** correct issue with multiple references to the same mzML file in one combination file such as created by iProphet. |
| + | ** Keep track on live threads and only join live threads. | ||
| + | * ''InteractParser:'' | ||
| + | ** Remove errorneous path from spectrum name when occurring | ||
| + | ** When the MS datafile not read in successfully don't try to access the spectrumList or it crashes. | ||
| * PTMProphet: BUGFIX better tracking of unspecified mods. fix reporting of masses combining a static and variable mod. | * PTMProphet: BUGFIX better tracking of unspecified mods. fix reporting of masses combining a static and variable mod. | ||
| * get_prots.pl: BUGFIX corrected pattern matching mistake, added JSON output. Include protein length in output. | * get_prots.pl: BUGFIX corrected pattern matching mistake, added JSON output. Include protein length in output. | ||
| + | * PG.html: fix highlighting and error histogram. | ||
| + | * PeptideProphetParser: If bad value in the model is found report and exit without generating giant log. | ||
| + | * ''PepXMLViewer.cgi:'' | ||
| + | ** Fix detection of libra result in current spectrum node (used for passing the Isobaric parameter to Lorikeet) | ||
| + | ** Fix link to plotspectrast | ||
| + | ** Fix reference to analysis file for spectrum name link (displays N top hits from engine) in Comet; use comet hits viewer for Sequest links | ||
| + | * iProphet: printing all_ntt_probs twice for ntt=0 caused a bug that is now fixed. | ||
| + | * InterProphet: improved handling of multiple threads. | ||
| + | * updatepaths.pl: Fixed an issue where the protein_summary_header element was not being updated | ||
| + | * updatepaths.pl: Replaced a conditional and (",") operator with a or ("|") operator so that the first update of an element is applied not the last | ||
| + | * Fixed an compilation issue with Boost 1.54 on Ubuntu via a patch to the Boost code. | ||
| + | * Corrected possible MacOS linker flag issue | ||
| + | * SpectraST: fixed a compilation issue on some platforms by explicitly casting a float to a int | ||
| + | * ''Petunia:'' | ||
| + | ** Removed Cygwin paths support | ||
| + | ** Removed unused Libra channel option | ||
| + | ** Replaced deprecated 'endform' with supported 'end_form' | ||
| + | ** Corrected an issue on Windows where Amazon Web Services credentials would not be accepted because they were being enclosed in quotes. | ||
| + | * ''tpp_models:'' | ||
| + | ** Only run on files with .xml extensions | ||
| == Miscellaneous == | == Miscellaneous == | ||
| - | + | * Updated d3 | |
| - | * Update d3 | + | * Corrected the source code headers to say "Institute for Systems Biology" not the "Insitute for Systems Biology". |
| + | * ''Libra'': Remove long-deprecated code (and get rid of unused LIBRA_GET_FROM_STDIN define). Cleaned up code spacing/formatting as well. | ||
| == Known Issues == | == Known Issues == | ||
| - | * ''No known issues to report'' | + | * Spectrast has a 2 GB file limit on Windows due to the use of C++ fstreams and the 32-bit libraries it is linked against. Certain Spectrast libraries such as the NIST_human_IT_2010_01_14_7AA.splib library may not work correctly when used with Spectrast. Users who encounter this issue can use specially built 64-bit version of Spectrast which can be found at in the [[http://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v0.0%20%28Development%29/ Sourceforge TPP development area]]. Simply download the “spectrast.exe” file there and replace the installed spectrast.exe with the one that you download. |
| + | |||
| + | == Getting the TPP Software == | ||
| + | |||
| + | * Download the TPP version 4.8.0 native windows installer (TPP_Setup_v4_8_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 4.8.0 source code .tgz package; | ||
| + | |||
| + | * Or, check out the code directly from svn: | ||
| + | svn checkout svn://svn.code.sf.net/p/sashimi/code/tags/release_4-8-0 | ||
| + | |||
| + | * For building from source, please refer to the README and INSTALL files in src/ directory of TPP as well as this wiki. | ||
| - | * For building from source, please refer to the readme file in TPP/src as well as the wiki. | + | == Acknowledgements == |
| 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. | 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. | ||
Current revision
Trans-Proteomic Pipeline (TPP) software, release 4.8.0 is a minor release of TPP that contains new features, improvements, and fixes to 4.7.1. The software is available for Windows as well as Linux (and unofficially) for OSX 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 on Linux or OS X, 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:4.7.1_Release_Notes
Contents |
[edit]
New Features
- ProteinProphet: GROUPWTS used by default now and OCCAMS razor is now sharper than with GROUPWTS before this change. For old GROUPWTS behavior use SOFTOCCAM option. NOGROUPWTS added for original behavior without GROUPWTS used. Also added count of distinct peptide sequences.
- ProteoGrapher: new tool for visualizing ProteinProphet prot.xml files in the context of Gene Ontology terms
- Petunia:
- Added page for idconvert (under new Files section)
- Added page for reSpect (under Utilities)
- Added page for running DNA to AA 6-frame translation utility
- Added drop-down for quick file select; points to dbase/ and speclibs where appropriate
- Point to new ProtXMLViewer as default; leave link to legacy viewer
- Allow search results to be written in directory other than where mz[X]ML files are:
- Comet and X!Tandem: use location of respective params file
- SpectraST: added input field for output dir (-sO option in SpaectraST)
- tpp_models:
- Support for charting ASAPRatio pvalue data and model
- Display ASAP mean ratio in linear (as well as default log)
- Added ability to highlight NSP bin and display peptide values alongside NSP table
- Added support for FPKM model info and Libra parameters
- The version string now contains Subversion revision information generated by the program svnversion.
[edit]
Improvements/Changes
- Comet: updated to version 2014.02 rev. 2
- PTMProphet: L[119] modification
- plotspectrast.cgi: set GNUPLOT_BINARY definition at build time
- Respect: cleanup some code, default minprob 0.5
- SpectraST: Peptide new mod for DiMethyl-C13HD2
- ASAPRatio:
- Enable wavelet option
- Write pvalue raw data and model into protXML file
- Lowered bin size on pvalue modeling from 0.05 to 0.02 (to get finer-grained model and values)
- xinteract:
- Run tpp_models.pl on all relevant files after the tmp directory shenanigans have taken place
- Got rid of suppoprt for ancient (perl) ProteinProphet
- Got rid of calls to extinct peptide and protein viewers
- Cleaned up usage statement
- Reformatted code to have consistent indentation; Other minor code cleanup
- Petunia
- Made dir listing much faster (by removing calls to extremely inefficient tpplib_perl for file extension checking)
- Broke out file browsing link (Files) to new section; moved updatePaths to this section
- Tool access menu items now span the entire row, with orange hover color
- Increased alpha opacity for menus
- Added 'dir_exists' validation
- Highlight (red color) the words 'warning' and 'error' when viewing command output
- Link bare .dta files to Lorikeet viewer
- Added new MS3 (Thermo) option to Libra
- Added link to ProteoGrapher for .prot.json files
- Added option to run ProteinProphet from iProphet page
- Test for amztpp prior to letting users enter their credentials
- Catch "ParserDetails.ini" line from amztpp when expecting an XML-only response
- Add error message as mouse-over when amz log-in fails
- Use '&' to separate commands in windows, move towards stripping out run_in
- ProtXMLViewer:
- Added NSP bin link (goes to models page, with extra URL params)
- Added charge state to peptide link to PepXMLViewer (to get better set of related spectra)
- Implemented generic support for Libra (removed hard-coded channel masses and related code)
- Added ability to sort by Libra channel
- Added distinction between 'n/a' quant ratios vs 'no result' (all peptides rejected)
- Added hard-coded secondary sort (by probability, or npeps)
- Changed 'peptides' to 'PSMs' in column heading
- Added support for Gaggle and JSON output -- and link to new ProteoGraphic tool
- Added basic command-line support
- Added 'single sequence entries' statistic
- Added option to display all peptides in single page (like old viewer)
- Warn user when no results passed filtering criteria
- Capture protein length
- Change cursor to 'wait' when loading data
- Minor formatting and css updates
- PepXMLViewer:
- Link PeptideProphet probability to new models page
- Auto run tpp_models if models page does not exist
- Remove link to more_pepanal.pl; replace with direct link to static html models page
- Replace hard-to-read ptm_peptide field (which had in-line probs for each potential AA) with a graphical bar-chart of probs above the peptide sequence -- with mouse-over site probs
- Highlight modified AAs in ptm peptide string
[edit]
Bug fixes
- RespectParser:
- Use stat to check for file's existence instead of try catch block that was crashing on windows.
- report each spectrum only once per file.
- correct issue with multiple references to the same mzML file in one combination file such as created by iProphet.
- Keep track on live threads and only join live threads.
- InteractParser:
- Remove errorneous path from spectrum name when occurring
- When the MS datafile not read in successfully don't try to access the spectrumList or it crashes.
- PTMProphet: BUGFIX better tracking of unspecified mods. fix reporting of masses combining a static and variable mod.
- get_prots.pl: BUGFIX corrected pattern matching mistake, added JSON output. Include protein length in output.
- PG.html: fix highlighting and error histogram.
- PeptideProphetParser: If bad value in the model is found report and exit without generating giant log.
- PepXMLViewer.cgi:
- Fix detection of libra result in current spectrum node (used for passing the Isobaric parameter to Lorikeet)
- Fix link to plotspectrast
- Fix reference to analysis file for spectrum name link (displays N top hits from engine) in Comet; use comet hits viewer for Sequest links
- iProphet: printing all_ntt_probs twice for ntt=0 caused a bug that is now fixed.
- InterProphet: improved handling of multiple threads.
- updatepaths.pl: Fixed an issue where the protein_summary_header element was not being updated
- updatepaths.pl: Replaced a conditional and (",") operator with a or ("|") operator so that the first update of an element is applied not the last
- Fixed an compilation issue with Boost 1.54 on Ubuntu via a patch to the Boost code.
- Corrected possible MacOS linker flag issue
- SpectraST: fixed a compilation issue on some platforms by explicitly casting a float to a int
- Petunia:
- Removed Cygwin paths support
- Removed unused Libra channel option
- Replaced deprecated 'endform' with supported 'end_form'
- Corrected an issue on Windows where Amazon Web Services credentials would not be accepted because they were being enclosed in quotes.
- tpp_models:
- Only run on files with .xml extensions
[edit]
Miscellaneous
- Updated d3
- Corrected the source code headers to say "Institute for Systems Biology" not the "Insitute for Systems Biology".
- Libra: Remove long-deprecated code (and get rid of unused LIBRA_GET_FROM_STDIN define). Cleaned up code spacing/formatting as well.
[edit]
Known Issues
- Spectrast has a 2 GB file limit on Windows due to the use of C++ fstreams and the 32-bit libraries it is linked against. Certain Spectrast libraries such as the NIST_human_IT_2010_01_14_7AA.splib library may not work correctly when used with Spectrast. Users who encounter this issue can use specially built 64-bit version of Spectrast which can be found at in the [Sourceforge TPP development area]. Simply download the “spectrast.exe” file there and replace the installed spectrast.exe with the one that you download.
[edit]
Getting the TPP Software
- Download the TPP version 4.8.0 native windows installer (TPP_Setup_v4_8_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 4.8.0 source code .tgz package;
- Or, check out the code directly from svn:
svn checkout svn://svn.code.sf.net/p/sashimi/code/tags/release_4-8-0
- For building from source, please refer to the README and INSTALL files in src/ directory of TPP as well as this wiki.
[edit]
Acknowledgements
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.
[edit]
SVN Log
The SVN log of all changes since the previous release are available at TPP:4.8.0_SVN_Log.
