TPP:4.6.0 Release Notes
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| == New Features == | == New Features == | ||
| - | * Support for use of Amazon Web Services in the Petunia interface | + | * ''PTMProphet'': new tool for assigning probabilities to PTM-sites |
| - | * ''Support for .mz5 format'' | + | * ''MSGFDB'' support |
| - | * Added a download button to the Petunia interface so that users can download a file or a zip archive of files directly from the browser. | + | * Support for ''.mz5'' format |
| - | * PTMProphet: new tool for assigning probabilities to PTM-sites | + | * 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. | ||
| - | * MSGFDB support | + | |
| + | * 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 == | ||
Revision as of 01:44, 31 August 2012
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.
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
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.
