TPP:4.5.1 Release Notes

From SPCTools

Trans-Proteomic Pipeline (TPP) "Rapture" 4.5.1 Release Notes

Trans-Proteomic Pipeline (TPP) software, release 4.5.1 is a maintenance release that addresses a number of issues found with 4.5.0. 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:4.5.0_Release_Notes

1 New Features
2 Improvements/Changes
3 Bug fixes
4 Miscellaneous
5 Known Issues
6 Getting the TPP Software
7 SVN Log

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New Features

[Petunia] New dynamic filtering box on file browser and chooser, with smart "select all" checkbox

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Improvements/Changes

Replace calls to pepxml_html2.pl with PepXMLViewer.cgi links (iProphet only...?)

Petunia:
- Added support for Bruker .yep and .baf files, as well as mzXML output to msconvert
- Expanded Libra normalization channel option to 8
- Reindex mzXML: new file with old name; rename old to: old-index
- Add ability to specify no output file for some commands
- auto cd to dir and strip out full path if all files in same dir (shorten command line) [xinteract only at the moment]
- Streamlined file operations buttons (Delete, Copy, Paste, etc)
- Display file extension being searched for in File Chooser
- Do not show Clipboard pane if empty
- Took out 'tilde' hack for XPRESS
- Decoy models pages now only ask for pep/protXML files as input
- Added version checking; warn users if using an old version of TPP
- Now using -nosticky pragma in perl CGI

[PepXMLViewer] Added link to Lorikeet spectrum viewer ("ions2")

Change xinteract to run RefreshParser before PeptideProphet

Have InteractParser detect if the search engine is OMSSA and if so apply the fix_pyro_mods_option automatically (do the right thing)

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Bug fixes

Potential code injection vulnerabilities addressed in a number of cgi programs

iProphet column renamed in PepXMLViewer.cgi (heading for PeptideProphet Probability and iProphet Probability were both called "probability")

Fixed iProphet models page ("performance" models were missing)

Fixed a memory issue in XPressPeptideParser that causes a potential seg fault during runtime.

Fixed buffer overrun in mzParser for rare cases where zlib compression increases file size.

Fix pepxml2html (view peptide hits) peptide link for SpectraST results. No longer calling this cgi

[Petunia] Fixed an issue where uploading files on Windows resulted in zero byte files.

[Petunia] Allow users to specify data dirs with leading uppercase (e.g. C:\blah\)

Includes a change by Brian to Proteowizard to address compilation issues under Linux/gcc 4.6.1

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Miscellaneous

Nothing to report

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Known Issues

None to report

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Getting the TPP Software

Download the TPP version 4.5.1 native windows installer (TPP_Setup_v4_5_RAPTURE_rev_1.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.

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