TPP:4.6.2 Release Notes
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| == Improvements/Changes == | == Improvements/Changes == | ||
| - | * Updated to latest Lorikeet MS/MS viewer. This corrected various bugs (i.e. fragment ion calculations) in the old viewer. Functionality also improved by optional peak picking algorithm for ion labeling which is checked on by default. | + | * Updated to latest ''Lorikeet'' MS/MS viewer. This corrected various bugs (i.e. fragment ion calculations) in the old viewer. Functionality also improved by optional peak picking algorithm for ion labeling which is checked on by default. |
| - | * Petunia now recognizes OMSSA generated pepXML files and displays a link to view the file in the pepXML viewer. OMSAA writes the older DOCTYPE DTD declaration in its XML output instead of using the XML schema declaration that Petunia was looking for. | + | * ''Petunia'' now recognizes OMSSA generated pepXML files and displays a link to view the file in the pepXML viewer. OMSAA writes the older DOCTYPE DTD declaration in its XML output instead of using the XML schema declaration that Petunia was looking for. |
| * TPP now recognizes the enzyme string "Trypsin/P". | * TPP now recognizes the enzyme string "Trypsin/P". | ||
| + | |||
| + | * Stop file checking in ''PepXMLViewer'' once a) file has been detected as changed on server, or b) 4 failed attempts at getting status. | ||
| == Bug fixes == | == Bug fixes == | ||
Revision as of 02:23, 7 February 2013
*** THIS DOCUMENT IS IN DRAFT FORM ***
Trans-Proteomic Pipeline (TPP) software, release 4.6.2 is a maintenance release of TPP that contains several fixes to 4.6.1. 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:4.6.1_Release_Notes
Contents |
New Features
- New dashboard page for the various prophets: visualize all pertinent models, error tables, run parameters, etc. Will displace current models page in next release.
- New decoy database generation tool: describe it??
Improvements/Changes
- Updated to latest Lorikeet MS/MS viewer. This corrected various bugs (i.e. fragment ion calculations) in the old viewer. Functionality also improved by optional peak picking algorithm for ion labeling which is checked on by default.
- Petunia now recognizes OMSSA generated pepXML files and displays a link to view the file in the pepXML viewer. OMSAA writes the older DOCTYPE DTD declaration in its XML output instead of using the XML schema declaration that Petunia was looking for.
- TPP now recognizes the enzyme string "Trypsin/P".
- Stop file checking in PepXMLViewer once a) file has been detected as changed on server, or b) 4 failed attempts at getting status.
Bug fixes
- Added a patch for the version of Boost bundled with TPP so that it will compile using gcc 4.7 (Ubuntu 10.12)
- Corrected an issue in ASAPRatio discovered when compiling with gcc 4.7 (Ubuntu 10.12). It was using of strcpy() and the source and destination overlapped in memory. According to the strcpy() reference one shouldn't do this so it was replaced with memmove().
- Added a patch for the version of HDF bundled with TPP so that it will compile using gcc 4.7 (Ubuntu 10.12)
- Corrected a issue with compiling under MingW/Windows with newer versions of g++. With Linux g++ version 4.1.2 the overloaded constructor construct is allowed but with g++ 4.6.2 on MingW it complains about having a constructor call itself. Regardless its unnecessary to have both constructors since the definition is assigning a default value to the last parameter anyhow.
- InteractParser no longer writes the alternate protein twice. This addresses an issue when running InteractParser on OMSSA results and then getting duplicate alternate proteins for a peptide.
- Updated the link to UniProtKB and removed the dead link to SGD from the protein page of the Comet viewer.
- ProtXML Viewer: Fixed links in tab-delimited output; got rid of ineffectual if statements; fixed a number of bad usage of variables (misnamed, uninitialized, redeclared, and unused); removed some old stale code and local (regis) path comparisons.
Miscellaneous
- No miscellaneous issues to report
Known Issues
- No known issues to report
Getting the TPP Software
- Download the TPP version 4.6.2 native windows installer (TPP_Setup_v4_6_2.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 4.6.2 source code .tgz package;
or, check out the code directly from svn:
"svn co http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-6-2"
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:4.6.2_SVN_Log.
