TPP:4.6.1 Release Notes
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| - | ''Trans-Proteomic Pipeline (TPP) "Occupy" 4.6.1 Release Notes''' | ||
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| Trans-Proteomic Pipeline (TPP) software, release 4.6.1 is a maintenance release of TPP that contains several fixes to 4.6.0. 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. | Trans-Proteomic Pipeline (TPP) software, release 4.6.1 is a maintenance release of TPP that contains several fixes to 4.6.0. 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. | ||
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| == Improvements/Changes == | == Improvements/Changes == | ||
| - | * '''X!Tandem (Cyclone)''' - Removed check for binary file formats; its function was to halt tandem if using a binary format (such as mz5). X!Tandem will now accept mz5 file input. | + | * ''X!Tandem (Cyclone)'' - Removed check for binary file formats; its function was to halt tandem if using a binary format (such as mz5). X!Tandem will now accept mz5 file input. |
| == Bug fixes == | == Bug fixes == | ||
| - | * BUG: [Tandem2XML] Applied patch provided by David Trudgian to correct an off by one size problem with file names that can cause Tandem2XML to segmentation fault. (Thanks David)! | + | * ''Tandem2XML'': |
| + | ** Applied patch provided by David Trudgian to correct an off by one size problem with file names that can cause a segmentation fault. (Thanks David!) | ||
| + | |||
| + | * ''PTMProphet'': | ||
| + | ** fixed issue that would cause a crash when the simplify call removes all peaks in the spectrum or the spectrum is empty | ||
| + | ** was being built but wasn't being installed on linux | ||
| - | * BUG: [PTMProphet] fixed issue that would cause a crash when the simplify call removes all peaks in the spectrum or the spectrum is empty | + | * ''X!Tandem (Cyclone)'': |
| + | ** fixed a problem that caps searches at charge 3 and below, regardless of user settings or known charge state. | ||
| + | ** fixed problem where X!Tandem neglects +4 possibility when precursor charge is unknown. | ||
| + | ** fixed a few pointer vs array memory frees reported by valgrind that have the potential to incur memory leaks or heap corruption on some platforms. | ||
| - | * BUG: [X!Tandem (Cyclone)] fixed a X!Tandem (Cyclone) problem that caps searches at charge 3 and below, regardless of user settings or known charge state. * | + | * ''mzParser'': |
| + | ** fixed incorrect return value in mz5 file loading when using mzParser interface instead of RAMP interface and made mz5 meta data parsing more robust. | ||
| - | * BUG: [X!Tandem (Cyclone)] fixed problem where X!tandem neglects +4 possibility when precursor charge is unknown. | + | * ''Mascot2XML'' |
| + | **The spectrum id is now written with 5 digit scan numbers instead of 4 in cases where no title is provided for the spectrum or scan numbers are present. There still may be situations were 4 digit scan numbers may occur in the pep.xml output files. | ||
| - | * BUG: [mzParser] Fixed incorrect return value in mz5 file loading when using mzParser interface instead of RAMP interface and made mz5 meta data parsing more robust. | + | * ''Petunia'': |
| + | ** Support multiple input files in pep and prots decoy validation pages; also, require ''decoy'' tag to be set | ||
| == Miscellaneous == | == Miscellaneous == | ||
Current revision
Trans-Proteomic Pipeline (TPP) software, release 4.6.1 is a maintenance release of TPP that contains several fixes to 4.6.0. 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:4.6.0_Release_Notes
Contents |
[edit]
New Features
- No new features to report
[edit]
Improvements/Changes
- X!Tandem (Cyclone) - Removed check for binary file formats; its function was to halt tandem if using a binary format (such as mz5). X!Tandem will now accept mz5 file input.
[edit]
Bug fixes
- Tandem2XML:
- Applied patch provided by David Trudgian to correct an off by one size problem with file names that can cause a segmentation fault. (Thanks David!)
- PTMProphet:
- fixed issue that would cause a crash when the simplify call removes all peaks in the spectrum or the spectrum is empty
- was being built but wasn't being installed on linux
- X!Tandem (Cyclone):
- fixed a problem that caps searches at charge 3 and below, regardless of user settings or known charge state.
- fixed problem where X!Tandem neglects +4 possibility when precursor charge is unknown.
- fixed a few pointer vs array memory frees reported by valgrind that have the potential to incur memory leaks or heap corruption on some platforms.
- mzParser:
- fixed incorrect return value in mz5 file loading when using mzParser interface instead of RAMP interface and made mz5 meta data parsing more robust.
- Mascot2XML
- The spectrum id is now written with 5 digit scan numbers instead of 4 in cases where no title is provided for the spectrum or scan numbers are present. There still may be situations were 4 digit scan numbers may occur in the pep.xml output files.
- Petunia:
- Support multiple input files in pep and prots decoy validation pages; also, require decoy tag to be set
[edit]
Miscellaneous
- No miscellaneous issues to report
[edit]
Known Issues
- No known issues to report
[edit]
Getting the TPP Software
- Download the TPP version 4.6.1 native windows installer (TPP_Setup_v4_6_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 4.6.1 source code .tgz package;
or, check out the code directly from svn:
"svn co http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-6-1"
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.
[edit]
SVN Log
The SVN log of all changes since the previous release are available at TPP:4.6.1_SVN_Log.
