TPP:4.8.0 Release Notes
From SPCTools
*** THIS IS A DRAFT DOCUMENT FOR DEVELOPERS ONLY ***
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
Contents |
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
- The version string now contains Subversion revision information generated by the program svnversion.
Improvements/Changes
- 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
- Comet: updated to version 2014.02 rev. 2
- tpp_gui.pl: use '&' to separate commands in windows, move towards stripping out run_in
Bug fixes
- RespectParser: Use stat to check for file's existence instead of try catch block that was crashing on windows.
- RespectParser: report each spectrum only once per file.
- RespectParser: correct issue with multiple references to the same mzML file in one combination file such as created by iProphet.
- RespectParser: Keep track on live threads and only join live threads.
- InteractParser: remove errorneous path from spectrum name when occurring
- InteractParser: BUGFIX 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: bug fix in parsing and display of PTMProphet data.
- 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/tpp_gui.pl: Fixed an issue with home page showing "reSpect" as a tab instead of "Utilities"
- Petunia/tpp_gui.pl: Corrected an issue on Windows whereas Amazon Web Services credentials would not be accepted because they were being enclosed in quotes.
Miscellaneous
- Update d3
- Corrected the source code headers to say "Institute for Systems Biology" not at the "Insitute for Systems Biology".
Known Issues
- No known issues to report
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 4.7.1 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 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:4.8.0_SVN_Log.
