TPP:4.6.0 SVN Log
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Changes since 4.5.2 release
------------------------------------------------------------------------ r5928 | real_procopio | 2012-08-16 16:31:14 -0700 (Thu, 16 Aug 2012) | 12 lines Amazon related changes: - Added option to run tandem search on the cloud - Added realclean (shut down and delete) button - Parse amztpp status from (new) xml output, new status page - New 'queued' command status - Monitoring code - New css classes to show queued jobs Added ability to specify multiple output files per command; New utility to display human readable file sizes; Specify SpectraST output to have '.pep.xml' suffix. ------------------------------------------------------------------------ r5926 | slagelwa | 2012-08-16 14:47:27 -0700 (Thu, 16 Aug 2012) | 2 lines Removing the RC ------------------------------------------------------------------------ r5921 | mhoopmann | 2012-08-08 16:13:14 -0700 (Wed, 08 Aug 2012) | 2 lines Corrected labeling of endian-ness. This is not a bug fix, just making the code easier to read. Performance is identical. Thanks Jimmy! ------------------------------------------------------------------------ r5917 | mhoopmann | 2012-07-18 09:17:35 -0700 (Wed, 18 Jul 2012) | 2 lines mzML and mzXML parsing bugfixes related to activation method. ------------------------------------------------------------------------ r5915 | slagelwa | 2012-07-03 16:10:57 -0700 (Tue, 03 Jul 2012) | 2 lines Taking out some debugging code I had left in ------------------------------------------------------------------------ r5914 | slagelwa | 2012-07-03 15:11:09 -0700 (Tue, 03 Jul 2012) | 2 lines Merging Mike r5913 change into branch ------------------------------------------------------------------------ r5912 | slagelwa | 2012-06-28 10:25:42 -0700 (Thu, 28 Jun 2012) | 5 lines * TPP's makefile has a "xtandem-debug" target that wasn't doing anything. Fixed this by using the value of DEBUG if its set. * Fixed a number of deallocation issues that valgrind was complaining about. ------------------------------------------------------------------------ r5911 | dshteyn | 2012-06-22 12:34:34 -0700 (Fri, 22 Jun 2012) | 1 line Remove xslt from link to XPressCGIProteinDisplayParser.cgi ------------------------------------------------------------------------ r5910 | dshteyn | 2012-06-22 12:33:20 -0700 (Fri, 22 Jun 2012) | 1 line XPressCGIProteinDisplayParser.cgi: fix obvious security issue with passing commands in QUERY_STRING ------------------------------------------------------------------------ r5908 | mhoopmann | 2012-06-19 10:59:14 -0700 (Tue, 19 Jun 2012) | 2 lines Report a,c,x,z ions (lost during upgrade to cyclone). Report N-terminal protein acetylation mods with the '[' symbol. ------------------------------------------------------------------------ r5907 | real_procopio | 2012-06-19 10:55:18 -0700 (Tue, 19 Jun 2012) | 1 line [Tandem2XML] Cleaner way to deal with N-term acetylation ------------------------------------------------------------------------ r5905 | slagelwa | 2012-06-18 14:54:35 -0700 (Mon, 18 Jun 2012) | 3 lines Increase the maximum number of threads allowed. Systems now exist with 16 or more cores. Why increase to 256? Why not? ------------------------------------------------------------------------ r5904 | slagelwa | 2012-06-18 11:49:45 -0700 (Mon, 18 Jun 2012) | 6 lines Disable indexing of file system by the browser by default. With this enabled it allows anyone to bypass the Petunia authentication/authoriation and both list and fetch any TPP data from a system that's been left open. This certainly doesn't close the door but it helps a little. ------------------------------------------------------------------------ r5901 | slagelwa | 2012-06-12 15:29:31 -0700 (Tue, 12 Jun 2012) | 5 lines Added download button to the filebrowser to allow downloading of files in a directory. Multiple files are downloaded as a zip file, single files as themselves. ------------------------------------------------------------------------ r5893 | slagelwa | 2012-06-04 16:21:57 -0700 (Mon, 04 Jun 2012) | 1 line ------------------------------------------------------------------------ r5891 | slagelwa | 2012-06-01 15:13:24 -0700 (Fri, 01 Jun 2012) | 3 lines Ubuntu's gcc doesn't like it when you don't catch the return value of fread() ------------------------------------------------------------------------ r5889 | mhoopmann | 2012-06-01 13:20:17 -0700 (Fri, 01 Jun 2012) | 1 line Minor changes to make sure tandem_native is identical with and without PLUGGABLE_SCORING. There is one remaining #ifdef PLUGGABLE_SCORING in mscore, however, it is handled in such a way that it should be identical when using "native". Tests show identical hyperscores, evalues, and peptide results. However, the section with the #ifdef PLUGGABLE_SCORING is not called at any point in any test I've tried. I cannot figure out how to trigger that section of code, which only relates to special cases for phosphosites. ------------------------------------------------------------------------ r5888 | real_procopio | 2012-06-01 12:57:42 -0700 (Fri, 01 Jun 2012) | 1 line [Tandem2XML] Deal with quick acetyl mods, default in Tandem as of 2010.01.01.1 ------------------------------------------------------------------------ r5886 | slagelwa | 2012-05-30 11:38:30 -0700 (Wed, 30 May 2012) | 1 line Bumping RC # ------------------------------------------------------------------------ r5885 | dshteyn | 2012-05-29 17:13:04 -0700 (Tue, 29 May 2012) | 1 line PTMProphet: Fix crash on peptides with modified 'n' written in the mod peptide tag. ------------------------------------------------------------------------ r5884 | dshteyn | 2012-05-29 17:00:56 -0700 (Tue, 29 May 2012) | 1 line put rename back in...it wasn't the problem ------------------------------------------------------------------------ r5883 | dshteyn | 2012-05-29 16:49:56 -0700 (Tue, 29 May 2012) | 1 line updateAllPaths.pl: Need to close open filehandles in windows to allow overwriting the existing file. ------------------------------------------------------------------------ r5882 | dshteyn | 2012-05-29 15:48:03 -0700 (Tue, 29 May 2012) | 1 line use a library to get current directory...system call to pwd stopped working ------------------------------------------------------------------------ r5880 | spacepod | 2012-05-24 15:16:33 -0700 (Thu, 24 May 2012) | 2 lines Small xtandem commandline build update: if only building TPP's xtandem in an otherwise clean source tree, be sure that the TPP's build directory is created too. ------------------------------------------------------------------------ r5879 | dshteyn | 2012-05-20 22:12:40 -0700 (Sun, 20 May 2012) | 1 line PTMProphet: Fix bug in enumerating all combinations of mods. Replaced recurring function with an iterative procedure. ------------------------------------------------------------------------ r5876 | dshteyn | 2012-05-17 11:50:47 -0700 (Thu, 17 May 2012) | 1 line PTMProphetParser: Switching to Binomial Distribution to compute probability to site being modified. Default settings: disable EM, enable MULTIPLEX ------------------------------------------------------------------------ r5875 | real_procopio | 2012-05-17 11:39:14 -0700 (Thu, 17 May 2012) | 1 line [Petunia] MULTIPLEX no longer an option in PTMProphet ------------------------------------------------------------------------ r5874 | real_procopio | 2012-05-16 16:49:12 -0700 (Wed, 16 May 2012) | 1 line [mzParser] start low, end high high as a kite! ------------------------------------------------------------------------ r5873 | mhoopmann | 2012-05-16 16:36:05 -0700 (Wed, 16 May 2012) | 3 lines conditional check on setting high and low mz ------------------------------------------------------------------------ r5872 | mhoopmann | 2012-05-16 16:30:55 -0700 (Wed, 16 May 2012) | 3 lines Updated mzXML parser to treat startMz and endMz attributes as synonymous to lowMz and highMz ------------------------------------------------------------------------ r5871 | dshteyn | 2012-05-16 15:41:18 -0700 (Wed, 16 May 2012) | 1 line ASAPRatio: Remove debugging output ------------------------------------------------------------------------ r5870 | spacepod | 2012-05-16 11:38:09 -0700 (Wed, 16 May 2012) | 1 line Minor cleanup: removing rouge tab character from Makefile.incl to prevent possible future make issues ------------------------------------------------------------------------ r5869 | dshteyn | 2012-05-16 11:16:19 -0700 (Wed, 16 May 2012) | 1 line tpp_gui.pl: Jobs page sorted by the Session with most recent job executed. Jobs within each session sorted in stack order. Makes it easier to find your job. ------------------------------------------------------------------------ r5868 | dshteyn | 2012-05-15 17:34:29 -0700 (Tue, 15 May 2012) | 1 line PTMProphet: further tweaks to enhance performance of the model ------------------------------------------------------------------------ r5867 | real_procopio | 2012-05-15 17:00:33 -0700 (Tue, 15 May 2012) | 1 line [PepXMLViewer] Fix webserver accessible file path ------------------------------------------------------------------------ r5866 | real_procopio | 2012-05-15 14:26:09 -0700 (Tue, 15 May 2012) | 1 line [lorikeet] Fix typos on parameter names for n- and c-terMods ------------------------------------------------------------------------ r5865 | real_procopio | 2012-05-15 14:20:38 -0700 (Tue, 15 May 2012) | 1 line [mascotout.pl] Added error message if file not found; also added html footer with TPP version ------------------------------------------------------------------------ r5864 | pcbrefugee | 2012-05-15 13:34:38 -0700 (Tue, 15 May 2012) | 1 line Branch copy of fix for an infinite recursion bug I introduced in trunk, change 5637 (Nov 2011). I missed it because I tend to use RAMP+pwiz instead of mzparser, surprising that it took anyone else this long to notice. Just a one liner to fix. Also backing out change 5854 to cached_ramp.h which was an attempt to fix this, and which led to performance hits in XPress and Libra (5853 is addressed XPress performance with changes equivalent to the #defines in cached_ramp.h, but Libra is still dinged) ------------------------------------------------------------------------ r5862 | real_procopio | 2012-05-14 20:08:45 -0700 (Mon, 14 May 2012) | 1 line [LibraPeptideParser] Re-formatting code so it can be read by human beings, no functional change ------------------------------------------------------------------------ r5860 | dshteyn | 2012-05-14 15:28:57 -0700 (Mon, 14 May 2012) | 1 line PTMProphet: model tweak ------------------------------------------------------------------------ r5858 | dshteyn | 2012-05-14 14:15:45 -0700 (Mon, 14 May 2012) | 1 line PTMProphetMpx: tweak to the model improves performance ------------------------------------------------------------------------ r5857 | spacepod | 2012-05-14 13:05:59 -0700 (Mon, 14 May 2012) | 1 line Removing zlib from build prerequisites on OS X; otherwise on make will error out on OS X (no target for -lz). zlib is still included in the linker flags for os x X!Tandem. NOTE: if zlib is not needed for some special platform such as mingw, it would be cleanest to remove this logic and simply remove ZLIB_LIB from the xtandem prereq list in both TPP and extern/xtandem makefiles. ------------------------------------------------------------------------ r5856 | dshteyn | 2012-05-14 13:01:43 -0700 (Mon, 14 May 2012) | 1 line New function for PTMProphet that remembers the peaks already matched ------------------------------------------------------------------------ r5855 | dshteyn | 2012-05-14 12:59:55 -0700 (Mon, 14 May 2012) | 1 line PTMProphet: Tweaking the algorithm to improve model ------------------------------------------------------------------------ r5854 | dshteyn | 2012-05-11 16:05:54 -0700 (Fri, 11 May 2012) | 1 line Commented out code causing an Infinite Recurrence ------------------------------------------------------------------------ r5853 | dshteyn | 2012-05-11 16:03:09 -0700 (Fri, 11 May 2012) | 1 line XPressPeptideParser: was slow, much faster using cached_ramp ------------------------------------------------------------------------ r5851 | real_procopio | 2012-05-10 14:33:38 -0700 (Thu, 10 May 2012) | 1 line [Petunia] Avoid doing the blinky thing on initial page load; also made blinking code more elegant (these things matter, yo!) ------------------------------------------------------------------------ r5850 | real_procopio | 2012-05-10 13:42:43 -0700 (Thu, 10 May 2012) | 1 line [Tandem2XML] Re-indented entire file for readibility, no functional change ------------------------------------------------------------------------ r5849 | dshteyn | 2012-05-10 11:32:39 -0700 (Thu, 10 May 2012) | 1 line Increase precision for reported intensities so even the tiny peaks can be seen...helpful for PTM assignment that depends on the small peaks ------------------------------------------------------------------------ r5848 | slagelwa | 2012-05-09 16:22:10 -0700 (Wed, 09 May 2012) | 14 lines Correction for building tandem w/pthreads as it was missing a dll. Turns out that in the past we were linking to the Windows version of threads even though we were building it in a Unix like environment provided by MinGW. This was accomplished by setting the define MSVC to fool the tandem build to think it was in a pure Windows environment...which of course is was not. This no longer works since the newest version of tandem has added some additional MS specific code (vector math)that is unavailable to MinGW. So instead of changing the tandem code to allow MS threads but not the math stuff I instead just built a pthreads version. Problem is that pthreads can only be build with a dynamic library (well *almost* true but for our purposes it might as well be). So we now include the pthreads dll in the installer. ------------------------------------------------------------------------ r5847 | real_procopio | 2012-05-09 15:59:18 -0700 (Wed, 09 May 2012) | 1 line [PepXMLViewer] Default ions2 link to Lorikeet, hide the link to old viewer (still available via Pick Columns) ------------------------------------------------------------------------ r5846 | real_procopio | 2012-05-09 15:44:49 -0700 (Wed, 09 May 2012) | 1 line [Petunia] Add blinking baloney when checking status on jobs page; Made MULTIPLEX the default for PTMProphet (as per DDS) ------------------------------------------------------------------------ r5845 | slagelwa | 2012-05-09 15:18:09 -0700 (Wed, 09 May 2012) | 5 lines Commented out EC2 special case in Makefile. Its no longer the default to detect that you are building on a EC2 node and need a special move to handle issues with using S3FS. If you need/want this functionality either uncomment the line in the Makefile.incl, or add the define on the command line. ------------------------------------------------------------------------ r5844 | dshteyn | 2012-05-09 14:54:13 -0700 (Wed, 09 May 2012) | 1 line ProphetModels.pl: BUGFIX double counting uniques ------------------------------------------------------------------------ r5843 | real_procopio | 2012-05-09 12:35:26 -0700 (Wed, 09 May 2012) | 1 line [Petunia] Fixed auto-refresh of page when submitting a job in Windows; Added ability to delete a single command output log file; Updated userTimeoutRecovery for new log files; Fixed small typo on PTMProphet page. ------------------------------------------------------------------------ r5842 | real_procopio | 2012-05-08 14:46:46 -0700 (Tue, 08 May 2012) | 1 line [plot-msms-js] Bugfix: do not attempt to populate ms1 data unless we are reading an mz[X]ML file ------------------------------------------------------------------------ r5841 | real_procopio | 2012-05-07 16:40:47 -0700 (Mon, 07 May 2012) | 1 line [Petunia] Specify output file to PTMProphet ------------------------------------------------------------------------ r5840 | slagelwa | 2012-05-07 16:32:35 -0700 (Mon, 07 May 2012) | 2 lines Merging another of David's changes in. ------------------------------------------------------------------------ r5838 | slagelwa | 2012-05-07 13:16:44 -0700 (Mon, 07 May 2012) | 2 lines Fixing compile issue with NEWPATH ------------------------------------------------------------------------ r5836 | dshteyn | 2012-05-07 12:10:59 -0700 (Mon, 07 May 2012) | 1 line Makefile for building PTMProphet MULTIPLEX ------------------------------------------------------------------------ r5835 | dshteyn | 2012-05-07 12:07:59 -0700 (Mon, 07 May 2012) | 1 line updateAllPaths.pl: switch to '\' to '/' for updating ------------------------------------------------------------------------ r5833 | real_procopio | 2012-05-07 11:02:18 -0700 (Mon, 07 May 2012) | 1 line [Petunia] Fix reported bug when converting multiple files to pepXML using semi-cleavage specificity ------------------------------------------------------------------------ r5832 | slagelwa | 2012-05-07 10:47:28 -0700 (Mon, 07 May 2012) | 2 lines Merging in David's latest check in on trunk into 4.6 ------------------------------------------------------------------------ r5821 | slagelwa | 2012-05-04 17:26:19 -0700 (Fri, 04 May 2012) | 2 lines Merging David's changes that were checked in on the trunk ------------------------------------------------------------------------ r5819 | real_procopio | 2012-05-04 15:39:06 -0700 (Fri, 04 May 2012) | 1 line [petunia] Added PTMProphet page (with a hack until the executable can handle output file as a parameter) ------------------------------------------------------------------------ r5816 | real_procopio | 2012-05-03 12:00:41 -0700 (Thu, 03 May 2012) | 1 line Added basic Amazon EC2 Management page: can register/delete keys and check status; Show 'no jobs' in Jobs status tooltip if none have been launched. ------------------------------------------------------------------------ r5815 | slagelwa | 2012-05-03 10:53:21 -0700 (Thu, 03 May 2012) | 1 line Adding PTM prophet to Windows installer file list ------------------------------------------------------------------------ r5814 | slagelwa | 2012-05-02 14:18:46 -0700 (Wed, 02 May 2012) | 2 lines .pl.pl should be .pl ------------------------------------------------------------------------ r5813 | slagelwa | 2012-05-02 12:01:45 -0700 (Wed, 02 May 2012) | 3 lines Tabs. Wicked. Tricksy. False. We hates Tabs. ------------------------------------------------------------------------ r5812 | slagelwa | 2012-05-02 10:14:31 -0700 (Wed, 02 May 2012) | 2 lines Adding rules for createChargeFile, mergeCharges and fileDownloader ------------------------------------------------------------------------ r5811 | slagelwa | 2012-05-01 11:00:39 -0700 (Tue, 01 May 2012) | 3 lines Merging David Shteynbergs recent change on the trunk into 4.6. ------------------------------------------------------------------------ r5809 | slagelwa | 2012-04-30 15:46:10 -0700 (Mon, 30 Apr 2012) | 2 lines Merging changes added on 4.5.2 branch after release ------------------------------------------------------------------------ r5804 | slagelwa | 2012-04-20 15:41:21 -0700 (Fri, 20 Apr 2012) | 2 lines * Fixed the patching of hdf5 * Set the version/build ------------------------------------------------------------------------ r5803 | slagelwa | 2012-04-19 14:57:34 -0700 (Thu, 19 Apr 2012) | 1 line [branch 4.6] creating the 4-6 branch from the trunk ------------------------------------------------------------------------
