From SPCTools
Changes since 4.5.2 release
------------------------------------------------------------------------
r5744 | dshteyn | 2012-02-07 16:38:46 -0800 (Tue, 07 Feb 2012) | 1 line
BUGFIX: didn't compile at linking step (Thanks Joe for the catch!)
------------------------------------------------------------------------
r5745 | slagelwa | 2012-02-08 13:40:39 -0800 (Wed, 08 Feb 2012) | 4 lines
Merging 4.5.2 changes into trunk. Fingers crossed. This should merge
only new changes from the branch that aren't already in the trunk.
------------------------------------------------------------------------
r5746 | slagelwa | 2012-02-09 14:02:27 -0800 (Thu, 09 Feb 2012) | 2 lines
Updated scripts for 4.5.2 release
------------------------------------------------------------------------
r5747 | slagelwa | 2012-02-09 14:18:14 -0800 (Thu, 09 Feb 2012) | 4 lines
Create the html/js directory so that we can copy files
to it.
------------------------------------------------------------------------
r5749 | slagelwa | 2012-02-10 14:20:08 -0800 (Fri, 10 Feb 2012) | 7 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".
------------------------------------------------------------------------
r5750 | slagelwa | 2012-02-15 12:21:52 -0800 (Wed, 15 Feb 2012) | 6 lines
* Fixed issue in stop pvm script where PVM enviroment variables weren't
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
------------------------------------------------------------------------
r5751 | slagelwa | 2012-02-15 16:52:06 -0800 (Wed, 15 Feb 2012) | 3 lines
Updated to use the latest version of Inspect. The one that was
being installed frequently core dumped.
------------------------------------------------------------------------
r5752 | slagelwa | 2012-02-16 13:21:48 -0800 (Thu, 16 Feb 2012) | 2 lines
Apply patch to fix buffer overflow problem in inspect
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
r5755 | slagelwa | 2012-03-01 14:23:12 -0800 (Thu, 01 Mar 2012) | 2 lines
Also install the qualscore lib directory
------------------------------------------------------------------------
r5756 | slagelwa | 2012-03-01 14:25:57 -0800 (Thu, 01 Mar 2012) | 2 lines
Fix copy
------------------------------------------------------------------------
r5757 | slagelwa | 2012-03-02 16:28:05 -0800 (Fri, 02 Mar 2012) | 8 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
------------------------------------------------------------------------
r5758 | slagelwa | 2012-03-06 09:05:56 -0800 (Tue, 06 Mar 2012) | 10 lines
"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.
------------------------------------------------------------------------
r5759 | slagelwa | 2012-03-06 18:25:44 -0800 (Tue, 06 Mar 2012) | 13 lines
Installs and tests pass on Windows.
* 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
------------------------------------------------------------------------
r5760 | slagelwa | 2012-03-07 16:51:25 -0800 (Wed, 07 Mar 2012) | 13 lines
* Cleaned up some issues with the AWS credentials
and finished reading optional region out of them
* Fixed a minor logging issue when logdie()
* Reworked amztppd to better handle credentials and
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
------------------------------------------------------------------------
r5763 | slagelwa | 2012-03-14 15:03:06 -0700 (Wed, 14 Mar 2012) | 7 lines
* Moved src_cyclone to src_gpm (the name cyclone will change). This is the copy
of tandem from gpm that we will modify.
* Moved src to src_hadoop. This is the tpp modifed version of tandem (cyclone)
that has Brian's hadoop work in it.
------------------------------------------------------------------------
r5764 | mhoopmann | 2012-03-14 15:24:36 -0700 (Wed, 14 Mar 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
------------------------------------------------------------------------
r5766 | mhoopmann | 2012-03-14 15:35:14 -0700 (Wed, 14 Mar 2012) | 1 line
Fixing makefile
------------------------------------------------------------------------
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
------------------------------------------------------------------------
r5768 | mhoopmann | 2012-03-14 16:43:07 -0700 (Wed, 14 Mar 2012) | 1 line
Turned off pluggable scoring definition in the code because it is defined at compile time.
------------------------------------------------------------------------
r5769 | mhoopmann | 2012-03-14 16:48:06 -0700 (Wed, 14 Mar 2012) | 1 line
Stupid no newline at end of file message...
------------------------------------------------------------------------
r5770 | mhoopmann | 2012-03-14 16:50:00 -0700 (Wed, 14 Mar 2012) | 1 line
Added Makefile for tpp x!tandem
------------------------------------------------------------------------
r5771 | mhoopmann | 2012-03-14 16:53:12 -0700 (Wed, 14 Mar 2012) | 3 lines
Updated makefile for tandem cyclone
------------------------------------------------------------------------
r5772 | mhoopmann | 2012-03-16 09:37:01 -0700 (Fri, 16 Mar 2012) | 1 line
Force mzXML base64 conversion to always be "network" even when specified otherwise, or not at all.
------------------------------------------------------------------------
r5779 | mhoopmann | 2012-03-29 13:03:55 -0700 (Thu, 29 Mar 2012) | 3 lines
Added mz5 file support; Works natively in the ramp interface. Also made other minor bugfixes and updates.
------------------------------------------------------------------------
r5780 | mhoopmann | 2012-03-29 13:09:38 -0700 (Thu, 29 Mar 2012) | 3 lines
Added hdf5 support files.
------------------------------------------------------------------------
r5781 | mhoopmann | 2012-03-29 13:11:47 -0700 (Thu, 29 Mar 2012) | 3 lines
removing hdf5 files not needed.
------------------------------------------------------------------------
r5782 | mhoopmann | 2012-03-29 13:13:26 -0700 (Thu, 29 Mar 2012) | 3 lines
Updating the makefiles to include HDF5 addition and changes to mzParser.
------------------------------------------------------------------------
r5783 | mhoopmann | 2012-03-30 12:08:28 -0700 (Fri, 30 Mar 2012) | 3 lines
More makefile fixes for HDF5 support
------------------------------------------------------------------------
r5784 | slagelwa | 2012-04-02 10:42:37 -0700 (Mon, 02 Apr 2012) | 4 lines
* Updated handling of qsub flags
* Some sequest updates
* Added qlog for showing contents of job log file using job id
------------------------------------------------------------------------
r5785 | mhoopmann | 2012-04-02 11:19:57 -0700 (Mon, 02 Apr 2012) | 2 lines
Fixed missing newline at end of file warnings. Added reading of chromatograms.
------------------------------------------------------------------------
r5786 | mhoopmann | 2012-04-02 12:24:25 -0700 (Mon, 02 Apr 2012) | 3 lines
Fixed makefiles
------------------------------------------------------------------------
r5787 | mhoopmann | 2012-04-02 12:25:29 -0700 (Mon, 02 Apr 2012) | 3 lines
Inserted more newlines at ends of files.
------------------------------------------------------------------------
r5789 | slagelwa | 2012-04-03 10:19:49 -0700 (Tue, 03 Apr 2012) | 2 lines
Nothing to see here. Move along.
------------------------------------------------------------------------
r5790 | mhoopmann | 2012-04-03 10:51:22 -0700 (Tue, 03 Apr 2012) | 3 lines
Adjusting the HDF5 linkage.
------------------------------------------------------------------------
r5791 | mhoopmann | 2012-04-03 11:50:50 -0700 (Tue, 03 Apr 2012) | 3 lines
Grr...
------------------------------------------------------------------------
r5792 | mhoopmann | 2012-04-03 12:16:24 -0700 (Tue, 03 Apr 2012) | 3 lines
More makefile fixes
------------------------------------------------------------------------
r5793 | mhoopmann | 2012-04-03 13:59:17 -0700 (Tue, 03 Apr 2012) | 3 lines
reversed ordering of HDF5 libraries
------------------------------------------------------------------------
r5794 | mhoopmann | 2012-04-03 14:49:15 -0700 (Tue, 03 Apr 2012) | 3 lines
Forgot to update this as well.
------------------------------------------------------------------------
r5795 | slagelwa | 2012-04-09 15:46:29 -0700 (Mon, 09 Apr 2012) | 27 lines
* 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
------------------------------------------------------------------------
r5796 | real_procopio | 2012-04-10 18:03:33 -0700 (Tue, 10 Apr 2012) | 12 lines
[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
------------------------------------------------------------------------
r5797 | slagelwa | 2012-04-11 13:48:53 -0700 (Wed, 11 Apr 2012) | 5 lines
* Fixed minor bug in Myrimatch when correcting scans
* Now outputs the error when a service reports one
* Updated version
------------------------------------------------------------------------
r5798 | slagelwa | 2012-04-12 16:29:59 -0700 (Thu, 12 Apr 2012) | 4 lines
Output a error message if we can't open the directory containing the
sequest output files, instead of segmentation faulting.
------------------------------------------------------------------------
r5799 | slagelwa | 2012-04-12 16:57:48 -0700 (Thu, 12 Apr 2012) | 2 lines
Checking in change again without eclipse reformatting tabs
------------------------------------------------------------------------
r5800 | slagelwa | 2012-04-13 13:49:05 -0700 (Fri, 13 Apr 2012) | 8 lines
* 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.
------------------------------------------------------------------------
r5801 | slagelwa | 2012-04-16 10:36:26 -0700 (Mon, 16 Apr 2012) | 3 lines
Fixing a small issue with regards to the file download retrys not actually
retrying on an error
------------------------------------------------------------------------
r5802 | slagelwa | 2012-04-18 15:34:59 -0700 (Wed, 18 Apr 2012) | 2 lines
Downgraded to HDF 1.8.6 (most recent version that builds in mingw)
Modifications to Makefile(s), headers, and sources to support building with hdf5 and mzParser changes in mingw
------------------------------------------------------------------------
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
------------------------------------------------------------------------
r5804 | slagelwa | 2012-04-20 15:41:21 -0700 (Fri, 20 Apr 2012) | 2 lines
* Fixed the patching of hdf5
* Set the version/build
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
r5812 | slagelwa | 2012-05-02 10:14:31 -0700 (Wed, 02 May 2012) | 2 lines
Adding rules for createChargeFile, mergeCharges and fileDownloader
------------------------------------------------------------------------
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
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.
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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!)
------------------------------------------------------------------------
r5853 | dshteyn | 2012-05-11 16:03:09 -0700 (Fri, 11 May 2012) | 1 line
XPressPeptideParser: was slow, much faster using cached_ramp
------------------------------------------------------------------------
r5854 | dshteyn | 2012-05-11 16:05:54 -0700 (Fri, 11 May 2012) | 1 line
Commented out code causing an Infinite Recurrence
------------------------------------------------------------------------
r5855 | dshteyn | 2012-05-14 12:59:55 -0700 (Mon, 14 May 2012) | 1 line
PTMProphet: Tweaking the algorithm to improve model
------------------------------------------------------------------------
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
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
r5858 | dshteyn | 2012-05-14 14:15:45 -0700 (Mon, 14 May 2012) | 1 line
PTMProphetMpx: tweak to the model improves performance
------------------------------------------------------------------------
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
[LibraPeptideParser] Re-formatting code so it can be read by human beings, no functional change
------------------------------------------------------------------------
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
[mascotout.pl] Added error message if file not found; also added html footer with TPP version
------------------------------------------------------------------------
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
------------------------------------------------------------------------
r5867 | real_procopio | 2012-05-15 17:00:33 -0700 (Tue, 15 May 2012) | 1 line
[PepXMLViewer] Fix webserver accessible file path
------------------------------------------------------------------------
r5868 | dshteyn | 2012-05-15 17:34:29 -0700 (Tue, 15 May 2012) | 1 line
PTMProphet: further tweaks to enhance performance of the model
------------------------------------------------------------------------
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
Minor cleanup: removing rouge tab character from Makefile.incl to prevent possible future make issues
------------------------------------------------------------------------
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
Updated mzXML parser to treat startMz and endMz attributes as synonymous to lowMz and highMz
------------------------------------------------------------------------
r5873 | mhoopmann | 2012-05-16 16:36:05 -0700 (Wed, 16 May 2012) | 3 lines
conditional check on setting high and low mz
------------------------------------------------------------------------
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!
------------------------------------------------------------------------
r5875 | real_procopio | 2012-05-17 11:39:14 -0700 (Thu, 17 May 2012) | 1 line
[Petunia] MULTIPLEX no longer an option in PTMProphet
------------------------------------------------------------------------
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
PTMProphet: Fix bug in enumerating all combinations of mods. Replaced recurring function with an iterative procedure.
------------------------------------------------------------------------
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
use a library to get current directory...system call to pwd stopped working
------------------------------------------------------------------------
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
put rename back in...it wasn't the problem
------------------------------------------------------------------------
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
[Tandem2XML] Deal with quick acetyl mods, default in Tandem as of 2010.01.01.1
------------------------------------------------------------------------
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
Ubuntu's gcc doesn't like it when you don't catch the
return value of fread()
------------------------------------------------------------------------
r5893 | slagelwa | 2012-06-04 16:21:57 -0700 (Mon, 04 Jun 2012) | 1 line
------------------------------------------------------------------------
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
------------------------------------------------------------------------
