TPP 4.1.1 maintanence release

[Natalie Tasman]

Hello all,

Most reported problems with Monday's 4.1.0 windows release have hopefully resolved, and TPP 4.1.1 is now available.  Most fixes are specifically for the Windows version; on all version, the interact.pep.shtml files are now correctly named (please see below).  Thanks to Brian Pratt, Luis, and David for these fixes.

You can safely install 4.1.1 over an existing 4.1.0 installation.

==4.1.1: maintenance release change log==

This is a bugfix-only release.  No new features are added.

* fix for bundled TPP version of tandem: fixes reported crash on windows

* fix for .shtml filename generation: files were incorrectly being generated as interact.shtml instead of interact.pep.shtml

* fix for Windows installer Perl version check: improved and more informative check for ActivePerl 5.8 or greater (which is now a Windows TPP requirment)

* fix for X!Tandem-to-pepXML conversion (Tandem2XML): scan names were generated incorrectly; detect if refinement was used; and set enzymatic constraint by detecting minimum allowed NTT setting in refinement mode, if enabled

Download the TPP version 4.1.1 native windows installer
(TPP_Setup_v4_1_JETSTREAM_rev_1.exe) from the Sashimi SourceForge
project file release page:
http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912

For downloading and installing the (older) Windows cygwin version please visit
the following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"

For downloading the source code, please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"
 or directly from svn: see
http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-1-1
Please refer to the readme file in TPP/src as well as the wiki.

Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/


The SPC Tools Team: Natalie, Luis, and David

-Natalie

[Natalie Tasman]

Another fix for Windows runsearch:

* fix for runsearch: correctly run certainly commands individually

-Natalie

[Natalie Tasman]

Hi all,

I'm updating the 4.1.1 Windows release with the correct version of msconvert.  The download will be unavailable for a short time.

-Natalie

[Natalie Tasman]

The Windows 4.1.1 installer, TPP_Setup_v4_1_JETSTREAM_rev_1.exe, has been updated with the correct version of msconvert.exe.  You only need to reinstall if you want to convert Thermo .raw files to mzML format.  No other changes were made.

You can download from http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912

Again, apologies for the inconvenience, and thanks to Oded for catching this.

Natalie