TPP:4.6.0 SVN Log

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<nowiki> <nowiki>
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-r5744 | dshteyn | 2012-02-07 16:38:46 -0800 (Tue, 07 Feb 2012) | 1 line+r5928 | real_procopio | 2012-08-16 16:31:14 -0700 (Thu, 16 Aug 2012) | 12 lines
-BUGFIX: didn't compile at linking step (Thanks Joe for the catch!)+Amazon related changes:
-------------------------------------------------------------------------+ - Added option to run tandem search on the cloud
-r5745 | slagelwa | 2012-02-08 13:40:39 -0800 (Wed, 08 Feb 2012) | 4 lines+ - Added realclean (shut down and delete) button
- + - Parse amztpp status from (new) xml output, new status page
-Merging 4.5.2 changes into trunk. Fingers crossed. This should merge+ - New 'queued' command status
-only new changes from the branch that aren't already in the trunk.+ - 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.
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-r5746 | slagelwa | 2012-02-09 14:02:27 -0800 (Thu, 09 Feb 2012) | 2 lines+r5926 | slagelwa | 2012-08-16 14:47:27 -0700 (Thu, 16 Aug 2012) | 2 lines
-Updated scripts for 4.5.2 release+Removing the RC
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-r5747 | slagelwa | 2012-02-09 14:18:14 -0800 (Thu, 09 Feb 2012) | 4 lines+r5921 | mhoopmann | 2012-08-08 16:13:14 -0700 (Wed, 08 Aug 2012) | 2 lines
- +
-Create the html/js directory so that we can copy files+
-to it.+
 +Corrected labeling of endian-ness. This is not a bug fix, just making the code easier to read. Performance is identical. Thanks Jimmy!
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-r5749 | slagelwa | 2012-02-10 14:20:08 -0800 (Fri, 10 Feb 2012) | 7 lines+r5917 | mhoopmann | 2012-07-18 09:17:35 -0700 (Wed, 18 Jul 2012) | 2 lines
- +
-* Added missing documentation on "-o" flag+
-* Fixed issue were ec2 node log file wasn't uploaded to S3. (Can't upload+
- the log file with the md5 as we are writing to it)+
-* Fixed an issue with abs_path resolving symbolic links. "We will not+
- resolve the link before its time".+
 +mzML and mzXML parsing bugfixes related to activation method.
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-r5750 | slagelwa | 2012-02-15 12:21:52 -0800 (Wed, 15 Feb 2012) | 6 lines+r5915 | slagelwa | 2012-07-03 16:10:57 -0700 (Tue, 03 Jul 2012) | 2 lines
-* Fixed issue in stop pvm script where PVM enviroment variables weren't+Taking out some debugging code I had left in
- exported.+
-* Added check to remove leftover pvm pid files+
-* Now saves the .dta and .out files in a tgz file so petunia interface+
- works again for showing top 10 hits+
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-r5751 | slagelwa | 2012-02-15 16:52:06 -0800 (Wed, 15 Feb 2012) | 3 lines+r5914 | slagelwa | 2012-07-03 15:11:09 -0700 (Tue, 03 Jul 2012) | 2 lines
-Updated to use the latest version of Inspect. The one that was+Merging Mike r5913 change into branch
-being installed frequently core dumped.+
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-r5752 | slagelwa | 2012-02-16 13:21:48 -0800 (Thu, 16 Feb 2012) | 2 lines+r5912 | slagelwa | 2012-06-28 10:25:42 -0700 (Thu, 28 Jun 2012) | 5 lines
-Apply patch to fix buffer overflow problem in inspect+* 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.
-r5753 | slagelwa | 2012-02-22 10:47:54 -0800 (Wed, 22 Feb 2012) | 7 lines+
- +
-Now requests a complex resource "sequest" that should be defined on each+
-host of 8 that will run sequest with a value of 8. This resource will prevent+
-more than one sequest job from running on the same node. Note that when you+
-request a PE with 8 slots you should request *1* resource as grid engine will+
-multiple the resource value by the # of requested slots in the PE.+
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-r5755 | slagelwa | 2012-03-01 14:23:12 -0800 (Thu, 01 Mar 2012) | 2 lines+r5911 | dshteyn | 2012-06-22 12:34:34 -0700 (Fri, 22 Jun 2012) | 1 line
- +
-Also install the qualscore lib directory+
 +Remove xslt from link to XPressCGIProteinDisplayParser.cgi
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-r5756 | slagelwa | 2012-03-01 14:25:57 -0800 (Thu, 01 Mar 2012) | 2 lines+r5910 | dshteyn | 2012-06-22 12:33:20 -0700 (Fri, 22 Jun 2012) | 1 line
- +
-Fix copy+
 +XPressCGIProteinDisplayParser.cgi: fix obvious security issue with passing commands in QUERY_STRING
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-r5757 | slagelwa | 2012-03-02 16:28:05 -0800 (Fri, 02 Mar 2012) | 8 lines+r5908 | mhoopmann | 2012-06-19 10:59:14 -0700 (Tue, 19 Jun 2012) | 2 lines
- +
- * replaced Net::Amazon::EC2 with VM::EC2 and all its goodness. Thanks,+
- Lincoln Stein. Now all we need is a VM::S3+
- * EC2 region now an option+
- * renamed stop() to terminate() to match EC2 API+
- * minor changes to amzbill+
- * Updated tests+
- +
 +Report a,c,x,z ions (lost during upgrade to cyclone).
 +Report N-terminal protein acetylation mods with the '[' symbol.
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-r5758 | slagelwa | 2012-03-06 09:05:56 -0800 (Tue, 06 Mar 2012) | 10 lines+r5907 | real_procopio | 2012-06-19 10:55:18 -0700 (Tue, 19 Jun 2012) | 1 line
- +
-"Mounts" a instance store disk partition on the EC2 instance. EC2 instance+
-root partitions are limited to 10GB. When amztpp was switched to using the+
-filesystem directly instead of a tmp directory the end result was that everything+
-was written to /, and this would fill up rather quickly. Now what it does+
-is always creates the root directory in /mnt (always one of the instance stores)+
-and mount --binds it to "/" so that the path appears like a normal path.+
- +
-Also removed the "-c" flag as its no longer applicable.+
- +
 +[Tandem2XML] Cleaner way to deal with N-term acetylation
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-r5759 | slagelwa | 2012-03-06 18:25:44 -0800 (Tue, 06 Mar 2012) | 13 lines+r5905 | slagelwa | 2012-06-18 14:54:35 -0700 (Mon, 18 Jun 2012) | 3 lines
-Installs and tests pass on Windows.+Increase the maximum number of threads allowed. Systems now exist with 16 or more cores. Why increase to 256? Why not?
-* Swapped out Proc::PID::File for File::Pid as the latter has 
- a ActiveState ppm 
-* Modified S3Manager so only unix paths are used in S3.  
- Get/Puts convert paths appropriately depending on platform 
-* Lot of work on the tests. Mainly skipping tests if they 
- don't have executables installed (e.g omssa) 
-* Some of the t/data files were not in the tarball 
-* Updated the message on credentials to "missing"  
- instead of invalid 
-  
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-r5760 | slagelwa | 2012-03-07 16:51:25 -0800 (Wed, 07 Mar 2012) | 13 lines+r5904 | slagelwa | 2012-06-18 11:49:45 -0700 (Mon, 18 Jun 2012) | 6 lines
-* Cleaned up some issues with the AWS credentials+Disable indexing of file system by the browser by default. With this enabled
-and finished reading optional region out of them+it allows anyone to bypass the Petunia authentication/authoriation and both
-* Fixed a minor logging issue when logdie()+list and fetch any TPP data from a system that's been left open. This certainly
-* Reworked amztppd to better handle credentials and+doesn't close the door but it helps a little.
- logging errors on them+
-* Log files on worker are correctly named by the+
- IP address of the worker in all cases+
-* Updated man documenation and included --region +
- paramter+
-* fixed tests to use credentials instead of +
- exception+
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-r5763 | slagelwa | 2012-03-14 15:03:06 -0700 (Wed, 14 Mar 2012) | 7 lines+r5901 | slagelwa | 2012-06-12 15:29:31 -0700 (Tue, 12 Jun 2012) | 5 lines
-* Moved src_cyclone to src_gpm (the name cyclone will change). This is the copy+Added download button to the filebrowser to allow downloading of files in a
-of tandem from gpm that we will modify.+directory. Multiple files are downloaded as a zip file, single files as
- +themselves.
-* Moved src to src_hadoop. This is the tpp modifed version of tandem (cyclone)+
- that has Brian's hadoop work in it.+
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-r5764 | mhoopmann | 2012-03-14 15:24:36 -0700 (Wed, 14 Mar 2012) | 1 line+r5893 | slagelwa | 2012-06-04 16:21:57 -0700 (Mon, 04 Jun 2012) | 1 line
-Updated TPP Tandem to Cyclone (Dec 2011 release) 
------------------------------------------------------------------------- 
-r5765 | mhoopmann | 2012-03-14 15:30:36 -0700 (Wed, 14 Mar 2012) | 1 line 
-Fixing diffs leftover from branch 
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-r5766 | mhoopmann | 2012-03-14 15:35:14 -0700 (Wed, 14 Mar 2012) | 1 line+r5891 | slagelwa | 2012-06-01 15:13:24 -0700 (Fri, 01 Jun 2012) | 3 lines
-Fixing makefile+Ubuntu's gcc doesn't like it when you don't catch the
-------------------------------------------------------------------------+return value of fread()
-r5767 | mhoopmann | 2012-03-14 16:22:37 -0700 (Wed, 14 Mar 2012) | 1 line+
-Updated objects to be prefixed with mzp to avoid confusion with X!Tandem 
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-r5768 | mhoopmann | 2012-03-14 16:43:07 -0700 (Wed, 14 Mar 2012) | 1 line+r5889 | mhoopmann | 2012-06-01 13:20:17 -0700 (Fri, 01 Jun 2012) | 1 line
-Turned off pluggable scoring definition in the code because it is defined at compile time.+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.
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-r5769 | mhoopmann | 2012-03-14 16:48:06 -0700 (Wed, 14 Mar 2012) | 1 line+r5888 | real_procopio | 2012-06-01 12:57:42 -0700 (Fri, 01 Jun 2012) | 1 line
-Stupid no newline at end of file message...+[Tandem2XML] Deal with quick acetyl mods, default in Tandem as of 2010.01.01.1
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-r5770 | mhoopmann | 2012-03-14 16:50:00 -0700 (Wed, 14 Mar 2012) | 1 line+r5886 | slagelwa | 2012-05-30 11:38:30 -0700 (Wed, 30 May 2012) | 1 line
-Added Makefile for tpp x!tandem+Bumping RC #
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-r5771 | mhoopmann | 2012-03-14 16:53:12 -0700 (Wed, 14 Mar 2012) | 3 lines+r5885 | dshteyn | 2012-05-29 17:13:04 -0700 (Tue, 29 May 2012) | 1 line
- +
-Updated makefile for tandem cyclone+
- +
 +PTMProphet: Fix crash on peptides with modified 'n' written in the mod peptide tag.
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-r5772 | mhoopmann | 2012-03-16 09:37:01 -0700 (Fri, 16 Mar 2012) | 1 line+r5884 | dshteyn | 2012-05-29 17:00:56 -0700 (Tue, 29 May 2012) | 1 line
-Force mzXML base64 conversion to always be "network" even when specified otherwise, or not at all.+put rename back in...it wasn't the problem
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-r5779 | mhoopmann | 2012-03-29 13:03:55 -0700 (Thu, 29 Mar 2012) | 3 lines+r5883 | dshteyn | 2012-05-29 16:49:56 -0700 (Tue, 29 May 2012) | 1 line
- +
-Added mz5 file support; Works natively in the ramp interface. Also made other minor bugfixes and updates.+
- +
 +updateAllPaths.pl: Need to close open filehandles in windows to allow overwriting the existing file.
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-r5780 | mhoopmann | 2012-03-29 13:09:38 -0700 (Thu, 29 Mar 2012) | 3 lines+r5882 | dshteyn | 2012-05-29 15:48:03 -0700 (Tue, 29 May 2012) | 1 line
- +
-Added hdf5 support files.+
- +
 +use a library to get current directory...system call to pwd stopped working
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-r5781 | mhoopmann | 2012-03-29 13:11:47 -0700 (Thu, 29 Mar 2012) | 3 lines+r5880 | spacepod | 2012-05-24 15:16:33 -0700 (Thu, 24 May 2012) | 2 lines
- +
-removing hdf5 files not needed.+
 +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.
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-r5782 | mhoopmann | 2012-03-29 13:13:26 -0700 (Thu, 29 Mar 2012) | 3 lines+r5879 | dshteyn | 2012-05-20 22:12:40 -0700 (Sun, 20 May 2012) | 1 line
- +
-Updating the makefiles to include HDF5 addition and changes to mzParser.+
- +
 +PTMProphet: Fix bug in enumerating all combinations of mods. Replaced recurring function with an iterative procedure.
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-r5783 | mhoopmann | 2012-03-30 12:08:28 -0700 (Fri, 30 Mar 2012) | 3 lines+r5876 | dshteyn | 2012-05-17 11:50:47 -0700 (Thu, 17 May 2012) | 1 line
- +
-More makefile fixes for HDF5 support+
- +
 +PTMProphetParser: Switching to Binomial Distribution to compute probability to site being modified. Default settings: disable EM, enable MULTIPLEX
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-r5784 | slagelwa | 2012-04-02 10:42:37 -0700 (Mon, 02 Apr 2012) | 4 lines+r5875 | real_procopio | 2012-05-17 11:39:14 -0700 (Thu, 17 May 2012) | 1 line
- +
-* Updated handling of qsub flags+
-* Some sequest updates+
-* Added qlog for showing contents of job log file using job id+
 +[Petunia] MULTIPLEX no longer an option in PTMProphet
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-r5785 | mhoopmann | 2012-04-02 11:19:57 -0700 (Mon, 02 Apr 2012) | 2 lines+r5874 | real_procopio | 2012-05-16 16:49:12 -0700 (Wed, 16 May 2012) | 1 line
- +
-Fixed missing newline at end of file warnings. Added reading of chromatograms.+
 +[mzParser] start low, end high high as a kite!
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-r5786 | mhoopmann | 2012-04-02 12:24:25 -0700 (Mon, 02 Apr 2012) | 3 lines+r5873 | mhoopmann | 2012-05-16 16:36:05 -0700 (Wed, 16 May 2012) | 3 lines
-Fixed makefiles+conditional check on setting high and low mz
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-r5787 | mhoopmann | 2012-04-02 12:25:29 -0700 (Mon, 02 Apr 2012) | 3 lines+r5872 | mhoopmann | 2012-05-16 16:30:55 -0700 (Wed, 16 May 2012) | 3 lines
-Inserted more newlines at ends of files.+Updated mzXML parser to treat startMz and endMz attributes as synonymous to lowMz and highMz
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-r5789 | slagelwa | 2012-04-03 10:19:49 -0700 (Tue, 03 Apr 2012) | 2 lines+r5871 | dshteyn | 2012-05-16 15:41:18 -0700 (Wed, 16 May 2012) | 1 line
- +
-Nothing to see here. Move along.+
 +ASAPRatio: Remove debugging output
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-r5790 | mhoopmann | 2012-04-03 10:51:22 -0700 (Tue, 03 Apr 2012) | 3 lines+r5870 | spacepod | 2012-05-16 11:38:09 -0700 (Wed, 16 May 2012) | 1 line
- +
-Adjusting the HDF5 linkage.+
- +
 +Minor cleanup: removing rouge tab character from Makefile.incl to prevent possible future make issues
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-r5791 | mhoopmann | 2012-04-03 11:50:50 -0700 (Tue, 03 Apr 2012) | 3 lines+r5869 | dshteyn | 2012-05-16 11:16:19 -0700 (Wed, 16 May 2012) | 1 line
- +
-Grr...+
- +
 +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.
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-r5792 | mhoopmann | 2012-04-03 12:16:24 -0700 (Tue, 03 Apr 2012) | 3 lines+r5868 | dshteyn | 2012-05-15 17:34:29 -0700 (Tue, 15 May 2012) | 1 line
- +
-More makefile fixes +
- +
 +PTMProphet: further tweaks to enhance performance of the model
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-r5793 | mhoopmann | 2012-04-03 13:59:17 -0700 (Tue, 03 Apr 2012) | 3 lines+r5867 | real_procopio | 2012-05-15 17:00:33 -0700 (Tue, 15 May 2012) | 1 line
- +
-reversed ordering of HDF5 libraries+
- +
 +[PepXMLViewer] Fix webserver accessible file path
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-r5794 | mhoopmann | 2012-04-03 14:49:15 -0700 (Tue, 03 Apr 2012) | 3 lines+r5866 | real_procopio | 2012-05-15 14:26:09 -0700 (Tue, 15 May 2012) | 1 line
- +
-Forgot to update this as well.+
- +
 +[lorikeet] Fix typos on parameter names for n- and c-terMods
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-r5795 | slagelwa | 2012-04-09 15:46:29 -0700 (Mon, 09 Apr 2012) | 27 lines+r5865 | real_procopio | 2012-05-15 14:20:38 -0700 (Tue, 15 May 2012) | 1 line
- +
-* Added new amztppservice for Windows. Manages aspects of installing+
- and removing the service. Turns out Windows doesn't like forking+
- daemons.+
-* Makefile.PL tries to add a amztpp service on Windows+
-* Correct dependencies are generated in the Makefile based+
- on installation platform+
-* Removed using CPAN ParallelManager as it blocks+
- on fork() and we can't have that on Windows. Implemented+
- own non-blocking forking of upload/downloads+
-* Files are now stored in S3 following a Unix convention+
- only and when coming from windows they are translated+
-* Output files are "fixed" to correct the paths when+
- copying back to windows from linux+
-* Bootstrap process streamlined+
-* Better "failsafe" using startup implemented for auto+
- shutting down nodes+
-* amztpp: can now save/delete user credentials for them+
-* amztpp: clean now realclean+
-* amztpp: only show first few files in S3 as opposed to all on+
- status command+
-* Updated man page, fixing grammer and outdated text+
-* Tests updated and additional tests added+
-* Copyrights updated+
-* Added warning notice to README disclaiming any responsibility+
- for expected or unexpected charges+
- +
 +[mascotout.pl] Added error message if file not found; also added html footer with TPP version
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-r5796 | real_procopio | 2012-04-10 18:03:33 -0700 (Tue, 10 Apr 2012) | 12 lines+r5864 | pcbrefugee | 2012-05-15 13:34:38 -0700 (Tue, 15 May 2012) | 1 line
- +
-[Petunia] Finished multiple commands monitoring:+
-- New jobs page, showing completed and running jobs, with links to view output, statuses are AJAX-updated+
-- New .jobs file to keep track of job status; only accessed/updated via file-locking+
-- Jobs menu title is AJAX-updated with status of all jobs, until all have been 'viewed' (also shown on tooltip with more text)+
-- Actions to support new AJAX requests+
-- Page Title shows number of running jobs (if any), AJAX-updated as well +
-- Handle multiple AJAX calls in a page via arrays+
-- New css classes for displaying command status+
-- Got rid of deprecated 'wait' and 'results' pages+
-- Cleaned up login page+
- +
 +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)
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-r5797 | slagelwa | 2012-04-11 13:48:53 -0700 (Wed, 11 Apr 2012) | 5 lines+r5862 | real_procopio | 2012-05-14 20:08:45 -0700 (Mon, 14 May 2012) | 1 line
- +
-* Fixed minor bug in Myrimatch when correcting scans+
-* Now outputs the error when a service reports one+
-* Updated version+
- +
 +[LibraPeptideParser] Re-formatting code so it can be read by human beings, no functional change
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-r5798 | slagelwa | 2012-04-12 16:29:59 -0700 (Thu, 12 Apr 2012) | 4 lines+r5860 | dshteyn | 2012-05-14 15:28:57 -0700 (Mon, 14 May 2012) | 1 line
- +
-Output a error message if we can't open the directory containing the+
-sequest output files, instead of segmentation faulting.+
- +
 +PTMProphet: model tweak
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-r5799 | slagelwa | 2012-04-12 16:57:48 -0700 (Thu, 12 Apr 2012) | 2 lines+r5858 | dshteyn | 2012-05-14 14:15:45 -0700 (Mon, 14 May 2012) | 1 line
- +
-Checking in change again without eclipse reformatting tabs+
 +PTMProphetMpx: tweak to the model improves performance
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-r5800 | slagelwa | 2012-04-13 13:49:05 -0700 (Fri, 13 Apr 2012) | 8 lines+r5857 | spacepod | 2012-05-14 13:05:59 -0700 (Mon, 14 May 2012) | 1 line
- +
-* Added the latest version of sequest+
-* Renamed the previous version to sequest27 as the architecture is+
- very different (threaded vs pvm)+
-* Always create the mgf file in the case of seach engines that need it. +
- Previously I was only creating it if it didn't exist. Which meant that+
- when you changed your search parameters the old values were still used.+
- +
 +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.
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-r5801 | slagelwa | 2012-04-16 10:36:26 -0700 (Mon, 16 Apr 2012) | 3 lines+r5856 | dshteyn | 2012-05-14 13:01:43 -0700 (Mon, 14 May 2012) | 1 line
- +
-Fixing a small issue with regards to the file download retrys not actually+
-retrying on an error+
 +New function for PTMProphet that remembers the peaks already matched
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-r5802 | slagelwa | 2012-04-18 15:34:59 -0700 (Wed, 18 Apr 2012) | 2 lines+r5855 | dshteyn | 2012-05-14 12:59:55 -0700 (Mon, 14 May 2012) | 1 line
-Downgraded to HDF 1.8.6 (most recent version that builds in mingw)+PTMProphet: Tweaking the algorithm to improve model
-Modifications to Makefile(s), headers, and sources to support building with hdf5 and mzParser changes in mingw+
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-r5803 | slagelwa | 2012-04-19 14:57:34 -0700 (Thu, 19 Apr 2012) | 1 line+r5854 | dshteyn | 2012-05-11 16:05:54 -0700 (Fri, 11 May 2012) | 1 line
-[branch 4.6] creating the 4-6 branch from the trunk+Commented out code causing an Infinite Recurrence
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-r5804 | slagelwa | 2012-04-20 15:41:21 -0700 (Fri, 20 Apr 2012) | 2 lines+r5853 | dshteyn | 2012-05-11 16:03:09 -0700 (Fri, 11 May 2012) | 1 line
-* Fixed the patching of hdf5+XPressPeptideParser: was slow, much faster using cached_ramp
-* Set the version/build+
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-r5809 | slagelwa | 2012-04-30 15:46:10 -0700 (Mon, 30 Apr 2012) | 2 lines+r5851 | real_procopio | 2012-05-10 14:33:38 -0700 (Thu, 10 May 2012) | 1 line
- +
-Merging changes added on 4.5.2 branch after release+
 +[Petunia] Avoid doing the blinky thing on initial page load; also made blinking code more elegant (these things matter, yo!)
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-r5811 | slagelwa | 2012-05-01 11:00:39 -0700 (Tue, 01 May 2012) | 3 lines+r5850 | real_procopio | 2012-05-10 13:42:43 -0700 (Thu, 10 May 2012) | 1 line
- +
-Merging David Shteynbergs recent change on the trunk into 4.6.+
- +
 +[Tandem2XML] Re-indented entire file for readibility, no functional change
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-r5812 | slagelwa | 2012-05-02 10:14:31 -0700 (Wed, 02 May 2012) | 2 lines+r5849 | dshteyn | 2012-05-10 11:32:39 -0700 (Thu, 10 May 2012) | 1 line
-Adding rules for createChargeFile, mergeCharges and fileDownloader+Increase precision for reported intensities so even the tiny peaks can be seen...helpful for PTM assignment that depends on the small peaks
- +
-------------------------------------------------------------------------+
-r5813 | slagelwa | 2012-05-02 12:01:45 -0700 (Wed, 02 May 2012) | 3 lines+
- +
-Tabs. Wicked. Tricksy. False. We hates Tabs.+
- +
- +
-------------------------------------------------------------------------+
-r5814 | slagelwa | 2012-05-02 14:18:46 -0700 (Wed, 02 May 2012) | 2 lines+
- +
-.pl.pl should be .pl+
- +
-------------------------------------------------------------------------+
-r5815 | slagelwa | 2012-05-03 10:53:21 -0700 (Thu, 03 May 2012) | 1 line+
- +
-Adding PTM prophet to Windows installer file list+
-------------------------------------------------------------------------+
-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.+
-------------------------------------------------------------------------+
-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)+
-------------------------------------------------------------------------+
-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+
- +
-------------------------------------------------------------------------+
-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+
- +
-------------------------------------------------------------------------+
-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+
-------------------------------------------------------------------------+
-r5835 | dshteyn | 2012-05-07 12:07:59 -0700 (Mon, 07 May 2012) | 1 line+
- +
-updateAllPaths.pl: switch to '\' to '/' for updating +
-------------------------------------------------------------------------+
-r5836 | dshteyn | 2012-05-07 12:10:59 -0700 (Mon, 07 May 2012) | 1 line+
- +
-Makefile for building PTMProphet MULTIPLEX+
-------------------------------------------------------------------------+
-r5838 | slagelwa | 2012-05-07 13:16:44 -0700 (Mon, 07 May 2012) | 2 lines+
- +
-Fixing compile issue with NEWPATH+
- +
-------------------------------------------------------------------------+
-r5840 | slagelwa | 2012-05-07 16:32:35 -0700 (Mon, 07 May 2012) | 2 lines+
- +
-Merging another of David's changes in.+
- +
-------------------------------------------------------------------------+
-r5841 | real_procopio | 2012-05-07 16:40:47 -0700 (Mon, 07 May 2012) | 1 line+
- +
-[Petunia] Specify output file to PTMProphet+
-------------------------------------------------------------------------+
-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+
-------------------------------------------------------------------------+
-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.+
-------------------------------------------------------------------------+
-r5844 | dshteyn | 2012-05-09 14:54:13 -0700 (Wed, 09 May 2012) | 1 line+
- +
-ProphetModels.pl: BUGFIX double counting uniques+
-------------------------------------------------------------------------+
-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.+
- +
-------------------------------------------------------------------------+
-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)+
-------------------------------------------------------------------------+
-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)+
------------------------------------------------------------------------ ------------------------------------------------------------------------
r5848 | slagelwa | 2012-05-09 16:22:10 -0700 (Wed, 09 May 2012) | 14 lines r5848 | slagelwa | 2012-05-09 16:22:10 -0700 (Wed, 09 May 2012) | 14 lines
Line 485: Line 255:
dll in the installer. dll in the installer.
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5849 | dshteyn | 2012-05-10 11:32:39 -0700 (Thu, 10 May 2012) | 1 line+r5847 | real_procopio | 2012-05-09 15:59:18 -0700 (Wed, 09 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+[PepXMLViewer] Default ions2 link to Lorikeet, hide the link to old viewer (still available via Pick Columns)
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5850 | real_procopio | 2012-05-10 13:42:43 -0700 (Thu, 10 May 2012) | 1 line+r5846 | real_procopio | 2012-05-09 15:44:49 -0700 (Wed, 09 May 2012) | 1 line
-[Tandem2XML] Re-indented entire file for readibility, no functional change+[Petunia] Add blinking baloney when checking status on jobs page; Made MULTIPLEX the default for PTMProphet (as per DDS)
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5851 | real_procopio | 2012-05-10 14:33:38 -0700 (Thu, 10 May 2012) | 1 line+r5845 | slagelwa | 2012-05-09 15:18:09 -0700 (Wed, 09 May 2012) | 5 lines
-[Petunia] Avoid doing the blinky thing on initial page load; also made blinking code more elegant (these things matter, yo!)+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
-r5853 | dshteyn | 2012-05-11 16:03:09 -0700 (Fri, 11 May 2012) | 1 line+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.
-XPressPeptideParser: was slow, much faster using cached_ramp 
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5854 | dshteyn | 2012-05-11 16:05:54 -0700 (Fri, 11 May 2012) | 1 line+r5844 | dshteyn | 2012-05-09 14:54:13 -0700 (Wed, 09 May 2012) | 1 line
-Commented out code causing an Infinite Recurrence+ProphetModels.pl: BUGFIX double counting uniques
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5855 | dshteyn | 2012-05-14 12:59:55 -0700 (Mon, 14 May 2012) | 1 line+r5843 | real_procopio | 2012-05-09 12:35:26 -0700 (Wed, 09 May 2012) | 1 line
-PTMProphet: Tweaking the algorithm to improve model+[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.
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5856 | dshteyn | 2012-05-14 13:01:43 -0700 (Mon, 14 May 2012) | 1 line+r5842 | real_procopio | 2012-05-08 14:46:46 -0700 (Tue, 08 May 2012) | 1 line
-New function for PTMProphet that remembers the peaks already matched+[plot-msms-js] Bugfix: do not attempt to populate ms1 data unless we are reading an mz[X]ML file
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5857 | spacepod | 2012-05-14 13:05:59 -0700 (Mon, 14 May 2012) | 1 line+r5841 | real_procopio | 2012-05-07 16:40:47 -0700 (Mon, 07 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.+[Petunia] Specify output file to PTMProphet
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5858 | dshteyn | 2012-05-14 14:15:45 -0700 (Mon, 14 May 2012) | 1 line+r5840 | slagelwa | 2012-05-07 16:32:35 -0700 (Mon, 07 May 2012) | 2 lines
-PTMProphetMpx: tweak to the model improves performance+Merging another of David's changes in.
-------------------------------------------------------------------------+
-r5860 | dshteyn | 2012-05-14 15:28:57 -0700 (Mon, 14 May 2012) | 1 line+
-PTMProphet: model tweak 
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5862 | real_procopio | 2012-05-14 20:08:45 -0700 (Mon, 14 May 2012) | 1 line+r5838 | slagelwa | 2012-05-07 13:16:44 -0700 (Mon, 07 May 2012) | 2 lines
-[LibraPeptideParser] Re-formatting code so it can be read by human beings, no functional change+Fixing compile issue with NEWPATH
-------------------------------------------------------------------------+
-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) 
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5865 | real_procopio | 2012-05-15 14:20:38 -0700 (Tue, 15 May 2012) | 1 line+r5836 | dshteyn | 2012-05-07 12:10:59 -0700 (Mon, 07 May 2012) | 1 line
-[mascotout.pl] Added error message if file not found; also added html footer with TPP version+Makefile for building PTMProphet MULTIPLEX
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5866 | real_procopio | 2012-05-15 14:26:09 -0700 (Tue, 15 May 2012) | 1 line+r5835 | dshteyn | 2012-05-07 12:07:59 -0700 (Mon, 07 May 2012) | 1 line
-[lorikeet] Fix typos on parameter names for n- and c-terMods+updateAllPaths.pl: switch to '\' to '/' for updating
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5867 | real_procopio | 2012-05-15 17:00:33 -0700 (Tue, 15 May 2012) | 1 line+r5833 | real_procopio | 2012-05-07 11:02:18 -0700 (Mon, 07 May 2012) | 1 line
-[PepXMLViewer] Fix webserver accessible file path+[Petunia] Fix reported bug when converting multiple files to pepXML using semi-cleavage specificity
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5868 | dshteyn | 2012-05-15 17:34:29 -0700 (Tue, 15 May 2012) | 1 line+r5832 | slagelwa | 2012-05-07 10:47:28 -0700 (Mon, 07 May 2012) | 2 lines
-PTMProphet: further tweaks to enhance performance of the model+Merging in David's latest check in on trunk into 4.6
-------------------------------------------------------------------------+
-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. 
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5870 | spacepod | 2012-05-16 11:38:09 -0700 (Wed, 16 May 2012) | 1 line+r5821 | slagelwa | 2012-05-04 17:26:19 -0700 (Fri, 04 May 2012) | 2 lines
-Minor cleanup: removing rouge tab character from Makefile.incl to prevent possible future make issues+Merging David's changes that were checked in on the trunk
-------------------------------------------------------------------------+
-r5871 | dshteyn | 2012-05-16 15:41:18 -0700 (Wed, 16 May 2012) | 1 line+
-ASAPRatio: Remove debugging output 
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5872 | mhoopmann | 2012-05-16 16:30:55 -0700 (Wed, 16 May 2012) | 3 lines+r5819 | real_procopio | 2012-05-04 15:39:06 -0700 (Fri, 04 May 2012) | 1 line
- +
-Updated mzXML parser to treat startMz and endMz attributes as synonymous to lowMz and highMz+
- +
 +[petunia] Added PTMProphet page (with a hack until the executable can handle output file as a parameter)
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5873 | mhoopmann | 2012-05-16 16:36:05 -0700 (Wed, 16 May 2012) | 3 lines+r5816 | real_procopio | 2012-05-03 12:00:41 -0700 (Thu, 03 May 2012) | 1 line
- +
-conditional check on setting high and low mz +
- +
 +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.
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5874 | real_procopio | 2012-05-16 16:49:12 -0700 (Wed, 16 May 2012) | 1 line+r5815 | slagelwa | 2012-05-03 10:53:21 -0700 (Thu, 03 May 2012) | 1 line
-[mzParser] start low, end high high as a kite!+Adding PTM prophet to Windows installer file list
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5875 | real_procopio | 2012-05-17 11:39:14 -0700 (Thu, 17 May 2012) | 1 line+r5814 | slagelwa | 2012-05-02 14:18:46 -0700 (Wed, 02 May 2012) | 2 lines
-[Petunia] MULTIPLEX no longer an option in PTMProphet+.pl.pl should be .pl
-------------------------------------------------------------------------+
-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 
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5879 | dshteyn | 2012-05-20 22:12:40 -0700 (Sun, 20 May 2012) | 1 line+r5813 | slagelwa | 2012-05-02 12:01:45 -0700 (Wed, 02 May 2012) | 3 lines
-PTMProphet: Fix bug in enumerating all combinations of mods. Replaced recurring function with an iterative procedure.+Tabs. Wicked. Tricksy. False. We hates Tabs.
-------------------------------------------------------------------------+
-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. 
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5882 | dshteyn | 2012-05-29 15:48:03 -0700 (Tue, 29 May 2012) | 1 line+r5812 | slagelwa | 2012-05-02 10:14:31 -0700 (Wed, 02 May 2012) | 2 lines
-use a library to get current directory...system call to pwd stopped working+Adding rules for createChargeFile, mergeCharges and fileDownloader
-------------------------------------------------------------------------+
-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. 
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5884 | dshteyn | 2012-05-29 17:00:56 -0700 (Tue, 29 May 2012) | 1 line+r5811 | slagelwa | 2012-05-01 11:00:39 -0700 (Tue, 01 May 2012) | 3 lines
-put rename back in...it wasn't the problem+Merging David Shteynbergs recent change on the trunk into 4.6.
-------------------------------------------------------------------------+
-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.  
------------------------------------------------------------------------- 
-r5886 | slagelwa | 2012-05-30 11:38:30 -0700 (Wed, 30 May 2012) | 1 line 
-Bumping RC # 
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5888 | real_procopio | 2012-06-01 12:57:42 -0700 (Fri, 01 Jun 2012) | 1 line+r5809 | slagelwa | 2012-04-30 15:46:10 -0700 (Mon, 30 Apr 2012) | 2 lines
-[Tandem2XML] Deal with quick acetyl mods, default in Tandem as of 2010.01.01.1+Merging changes added on 4.5.2 branch after release
-------------------------------------------------------------------------+
-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. 
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5891 | slagelwa | 2012-06-01 15:13:24 -0700 (Fri, 01 Jun 2012) | 3 lines+r5804 | slagelwa | 2012-04-20 15:41:21 -0700 (Fri, 20 Apr 2012) | 2 lines
- +
-Ubuntu's gcc doesn't like it when you don't catch the+
-return value of fread()+
 +* Fixed the patching of hdf5
 +* Set the version/build
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5893 | slagelwa | 2012-06-04 16:21:57 -0700 (Mon, 04 Jun 2012) | 1 line+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
------------------------------------------------------------------------ ------------------------------------------------------------------------
-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. 
- 
- 
------------------------------------------------------------------------- 
-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. 
- 
- 
------------------------------------------------------------------------- 
-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? 
- 
- 
------------------------------------------------------------------------- 
-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 
------------------------------------------------------------------------- 
-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. 
------------------------------------------------------------------------- 
-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 
------------------------------------------------------------------------- 
-r5911 | dshteyn | 2012-06-22 12:34:34 -0700 (Fri, 22 Jun 2012) | 1 line 
- 
-Remove xslt from link to XPressCGIProteinDisplayParser.cgi 
------------------------------------------------------------------------- 
-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. 
- 
- 
------------------------------------------------------------------------- 
-r5914 | slagelwa | 2012-07-03 15:11:09 -0700 (Tue, 03 Jul 2012) | 2 lines 
- 
-Merging Mike r5913 change into branch 
- 
------------------------------------------------------------------------- 
</nowiki> </nowiki>

Current revision

[edit]

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
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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
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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)
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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
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r5860 | dshteyn | 2012-05-14 15:28:57 -0700 (Mon, 14 May 2012) | 1 line

PTMProphet: model tweak
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r5858 | dshteyn | 2012-05-14 14:15:45 -0700 (Mon, 14 May 2012) | 1 line

PTMProphetMpx: tweak to the model improves performance
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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.
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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
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r5855 | dshteyn | 2012-05-14 12:59:55 -0700 (Mon, 14 May 2012) | 1 line

PTMProphet: Tweaking the algorithm to improve model
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r5854 | dshteyn | 2012-05-11 16:05:54 -0700 (Fri, 11 May 2012) | 1 line

Commented out code causing an Infinite Recurrence
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r5853 | dshteyn | 2012-05-11 16:03:09 -0700 (Fri, 11 May 2012) | 1 line

XPressPeptideParser: was slow, much faster using cached_ramp
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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!)
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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
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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
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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.
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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)
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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)
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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.

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r5844 | dshteyn | 2012-05-09 14:54:13 -0700 (Wed, 09 May 2012) | 1 line

ProphetModels.pl:  BUGFIX double counting uniques
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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.
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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
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r5841 | real_procopio | 2012-05-07 16:40:47 -0700 (Mon, 07 May 2012) | 1 line

[Petunia] Specify output file to PTMProphet
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r5840 | slagelwa | 2012-05-07 16:32:35 -0700 (Mon, 07 May 2012) | 2 lines

Merging another of David's changes in.

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r5838 | slagelwa | 2012-05-07 13:16:44 -0700 (Mon, 07 May 2012) | 2 lines

Fixing compile issue with NEWPATH

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r5836 | dshteyn | 2012-05-07 12:10:59 -0700 (Mon, 07 May 2012) | 1 line

Makefile for building PTMProphet MULTIPLEX
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r5835 | dshteyn | 2012-05-07 12:07:59 -0700 (Mon, 07 May 2012) | 1 line

updateAllPaths.pl: switch to '\' to '/' for updating 
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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
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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

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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

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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)
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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.
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r5815 | slagelwa | 2012-05-03 10:53:21 -0700 (Thu, 03 May 2012) | 1 line

Adding PTM prophet to Windows installer file list
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r5814 | slagelwa | 2012-05-02 14:18:46 -0700 (Wed, 02 May 2012) | 2 lines

.pl.pl should be .pl

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r5813 | slagelwa | 2012-05-02 12:01:45 -0700 (Wed, 02 May 2012) | 3 lines

Tabs.  Wicked. Tricksy. False.  We hates Tabs.


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r5812 | slagelwa | 2012-05-02 10:14:31 -0700 (Wed, 02 May 2012) | 2 lines

Adding rules for createChargeFile, mergeCharges and fileDownloader

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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.


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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

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r5804 | slagelwa | 2012-04-20 15:41:21 -0700 (Fri, 20 Apr 2012) | 2 lines

* Fixed the patching of hdf5
* Set the version/build
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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
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