TPP:4.4.0 Release Notes

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=== eng_jk === === eng_jk ===
-------------------------------------------------------------------------+<b>XPRESS</b>
-r5031 | eng_jk | 2010-06-10 10:22:48 -0700 (Thu, 10 Jun 2010) | 1 line+
 +Added support for intensity ratios (versus area based ratios) and specifying negative mass offsets. XPRESS includes better support for highres data by optionally summing individual isotope peaks for chromatogram reconstruction.
-------------------------------------------------------------------------+Added minimum chromatrogram ion count parameter -c<num>. This parameter filters out entries from being quantified unless the reconstruction chromatogram meets the minimum number of peaks specified.
-r5030 | eng_jk | 2010-06-10 10:12:50 -0700 (Thu, 10 Jun 2010) | 2 lines+
-change default last scan to big value+Added -l label free option. This option will calculate stats on precursor ions only. Resulting analysis is labeled as 'xpresslabelfree' in pep.xml.
------------------------------------------------------------------------- 
-r5029 | eng_jk | 2010-06-10 09:12:26 -0700 (Thu, 10 Jun 2010) | 2 lines 
-add option to remove N-term methionine+<b>MzXML2Search</b>
-------------------------------------------------------------------------+Add -N option to print out top N most intense peaks in a spectrum. Needed for large peaklists from new instrument as Mascot will complain if input peak list exceeds 10,000 count.
-r5003 | eng_jk | 2010-06-02 12:16:48 -0700 (Wed, 02 Jun 2010) | 2 lines+
-add support to zooming into TMT reporter region 
- 
------------------------------------------------------------------------- 
-r4999 | eng_jk | 2010-05-31 20:08:39 -0700 (Mon, 31 May 2010) | 2 lines 
- 
-add RTINSECONDS to mgf output 
- 
------------------------------------------------------------------------- 
-r4997 | eng_jk | 2010-05-28 13:35:43 -0700 (Fri, 28 May 2010) | 2 lines 
- 
-also pulled out the accession in the deflines in the contaminant files that get appended to each database 
- 
------------------------------------------------------------------------- 
-r4996 | eng_jk | 2010-05-28 13:20:29 -0700 (Fri, 28 May 2010) | 2 lines 
- 
-just pull accession as first word in defline 
- 
------------------------------------------------------------------------- 
-r4976 | eng_jk | 2010-05-14 08:52:28 -0700 (Fri, 14 May 2010) | 2 lines 
- 
-update script to grab uniprot (sprot and trembl) and create subsets with contaminants 
- 
------------------------------------------------------------------------- 
-r4973 | eng_jk | 2010-05-11 16:28:56 -0700 (Tue, 11 May 2010) | 2 lines 
- 
-update phosphate loss peaks highlighting; highlighting happens when 'Phos=1' present on URL 
- 
------------------------------------------------------------------------- 
-r4970 | eng_jk | 2010-05-07 17:01:08 -0700 (Fri, 07 May 2010) | 2 lines 
- 
-fix -M metabolic heavy function; chromatograms endpoints were being based on the light chromatograms and not the heavy chromatograms  
- 
------------------------------------------------------------------------- 
-r4968 | eng_jk | 2010-05-06 07:53:18 -0700 (Thu, 06 May 2010) | 2 lines 
- 
-add in -nodta option to create archive of .out only and not include the spectra 
- 
------------------------------------------------------------------------- 
-r4966 | eng_jk | 2010-04-28 15:12:10 -0700 (Wed, 28 Apr 2010) | 2 lines 
- 
-update new command line options for xpress; forgot to include this in prev checkin 
- 
------------------------------------------------------------------------- 
-r4965 | eng_jk | 2010-04-28 15:11:13 -0700 (Wed, 28 Apr 2010) | 17 lines 
- 
-[xpress] Add -l label free option. 
- 
-This option will calculate stats on precursor ions only. 
-Resulting analysis is labeled as 'xpresslabelfree' in pep.xml. 
-When using this option, every precursor that passes filters such as minimum peaks will get 
-an xpresslabelfree_result element that contains 
-- first_scan scan # of chromatographic peak start 
-- last_scan scan # of chromatographic peak end 
-- first_scan_RT_seconds retention time of chromatographic peak start 
-- last_scan_RT_seconds retention time of chromatographic peak end 
-- precursor_mz precursor m/z  
-- peak_area sum peak area 
-- peak_intensity maximum intensity (presumably at peak apex) 
-- peak_intensity_RT_seconds retention time of maximum intensity 
-- peak_intensity_scan scan number of maximum intensity 
- 
- 
------------------------------------------------------------------------- 
-r4964 | eng_jk | 2010-04-28 14:58:23 -0700 (Wed, 28 Apr 2010) | 1 line 
- 
- 
------------------------------------------------------------------------- 
-r4963 | eng_jk | 2010-04-27 17:05:15 -0700 (Tue, 27 Apr 2010) | 2 lines 
- 
-correct 'chymotryptic' to 'chymotrypsin' 
- 
------------------------------------------------------------------------- 
-r4961 | eng_jk | 2010-04-23 15:38:48 -0700 (Fri, 23 Apr 2010) | 2 lines 
- 
-add -P option to print out normalized intensity values for neutral loss masses associated with phosphate loss 
- 
------------------------------------------------------------------------- 
-r4945 | eng_jk | 2010-04-15 13:02:28 -0700 (Thu, 15 Apr 2010) | 2 lines 
- 
-parsing update for entry with protein n-term modification which doesn't seem to be handled by current code 
- 
------------------------------------------------------------------------- 
-r4942 | eng_jk | 2010-04-14 10:37:16 -0700 (Wed, 14 Apr 2010) | 2 lines 
- 
-remove tilde hack; i'll deal with the issue (dashes for negative numbers not being argument delimiters when all args are concatenated together in xinteract) upstream of xpress when needed 
- 
------------------------------------------------------------------------- 
-r4941 | eng_jk | 2010-04-14 10:13:25 -0700 (Wed, 14 Apr 2010) | 2 lines 
- 
-this should've gone with commit 4940 to support intensity based ratios 
- 
------------------------------------------------------------------------- 
-r4940 | eng_jk | 2010-04-13 17:33:35 -0700 (Tue, 13 Apr 2010) | 2 lines 
- 
-add support for intensity ratios and specifying negative mass offsets 
- 
------------------------------------------------------------------------- 
-r4923 | eng_jk | 2010-03-31 21:18:50 -0700 (Wed, 31 Mar 2010) | 3 lines 
- 
-[mzxml2search] Add -N option to print out top N most intense peaks in a spectrum; needed for large peaklists from new instruments. 
-Also add logic to semi-properly handle application of both minimum intensity filter and minimum peak count. 
- 
------------------------------------------------------------------------- 
-r4904 | eng_jk | 2010-03-15 16:58:28 -0700 (Mon, 15 Mar 2010) | 2 lines 
- 
-make the peaklist mass and intensity precisions a user defined option with -pm<num> -pi<num> 
- 
------------------------------------------------------------------------- 
-r4903 | eng_jk | 2010-03-15 16:26:32 -0700 (Mon, 15 Mar 2010) | 2 lines 
- 
-update help text to add/clarify description of output columns 
- 
------------------------------------------------------------------------- 
-r4900 | eng_jk | 2010-03-11 09:58:18 -0800 (Thu, 11 Mar 2010) | 2 lines 
- 
-dynamically allocate large arrays to address memory issues 
- 
------------------------------------------------------------------------- 
-r4873 | eng_jk | 2010-02-10 18:28:37 -0800 (Wed, 10 Feb 2010) | 2 lines 
- 
-add missing mass filter to ms2 and odta output; change default max mass to 5K 
- 
------------------------------------------------------------------------- 
-r4869 | eng_jk | 2010-02-09 22:15:08 -0800 (Tue, 09 Feb 2010) | 2 lines 
- 
-fix wrong mass used for 3rd modification mass 
- 
------------------------------------------------------------------------- 
-r4864 | eng_jk | 2010-01-28 01:13:14 -0800 (Thu, 28 Jan 2010) | 2 lines 
- 
-found .out file where incomplete header date killed parsing; simple workaround 
- 
------------------------------------------------------------------------- 
-r4862 | eng_jk | 2010-01-21 16:04:32 -0800 (Thu, 21 Jan 2010) | 2 lines 
- 
-change triangle polygons to vertical lines in chromatogram display 
- 
------------------------------------------------------------------------- 
-r4861 | eng_jk | 2010-01-21 15:34:53 -0800 (Thu, 21 Jan 2010) | 2 lines 
- 
-tweak filter params 
- 
------------------------------------------------------------------------- 
-r4860 | eng_jk | 2010-01-21 14:33:35 -0800 (Thu, 21 Jan 2010) | 2 lines 
- 
-[xpress] modify butterworth filter to not give as tight of fit to smoothed (low-pass) curve; modify chromatogram display to show larger scan range 
- 
------------------------------------------------------------------------- 
-r4803 | eng_jk | 2009-12-21 11:52:02 -0800 (Mon, 21 Dec 2009) | 2 lines 
- 
-extra period being appended to generated pep.shtml link 
- 
------------------------------------------------------------------------- 
-r4802 | eng_jk | 2009-12-18 10:42:33 -0800 (Fri, 18 Dec 2009) | 4 lines 
- 
-also scale precursor for large image 
-make y-ions red and b-ions blue to conform to pseudo standard 
-fix ugly errors in output when chosen but nothing to plot for E-value chart 
- 
------------------------------------------------------------------------- 
-r4794 | eng_jk | 2009-12-10 18:12:33 -0800 (Thu, 10 Dec 2009) | 2 lines 
- 
-[readw] add LTQ Velos and TSQ Vantage to instrument types; sadly both LTQ Velos and LTQ Orbitrap Velos report as "LTQ Velos" using GetInstModel() 
- 
------------------------------------------------------------------------- 
-r4783 | eng_jk | 2009-11-25 11:08:32 -0800 (Wed, 25 Nov 2009) | 2 lines 
- 
-[xpress] correctly calculate m/z with more precision in update CGI 
- 
------------------------------------------------------------------------- 
-r4782 | eng_jk | 2009-11-24 10:18:32 -0800 (Tue, 24 Nov 2009) | 2 lines 
- 
-[xpress] additional mods for quantification using individual isotope peak chromatograms 
- 
------------------------------------------------------------------------- 
-r4778 | eng_jk | 2009-11-18 13:40:19 -0800 (Wed, 18 Nov 2009) | 2 lines 
- 
-[sqt2xml] use get_pepxml_dot_ext() to derive output pep.xml extension 
- 
------------------------------------------------------------------------- 
-r4777 | eng_jk | 2009-11-18 11:43:54 -0800 (Wed, 18 Nov 2009) | 8 lines 
- 
-[sqt2xml] updates contributed by Mike Coleman including 
-- define proton mass using double-precision constant 
-- trim whitespace from SEQUEST output to give correct peptide  
-- trim locus, defensively  
-- default DeltaCn is 0 (not 1)  
-- require only one argument  
-- change created file extension from .pepXML to .pep.xml [JKE] 
- 
------------------------------------------------------------------------- 
-r4766 | eng_jk | 2009-11-13 10:40:56 -0800 (Fri, 13 Nov 2009) | 2 lines 
- 
-[out2xml] add support for another variant of n- and c-term variable mods 
- 
------------------------------------------------------------------------- 
-r4765 | eng_jk | 2009-11-13 10:31:50 -0800 (Fri, 13 Nov 2009) | 2 lines 
- 
-[xpress] revert changes made in revision 1177. Set minimum peptide probabilities for contributing to protein ratio. Without this change, ratios for incorrect peptide assignments contribute to the protein ratio. 
- 
------------------------------------------------------------------------- 
-r4764 | eng_jk | 2009-11-13 10:15:06 -0800 (Fri, 13 Nov 2009) | 2 lines 
- 
-add support for tracking individual isotope peaks for chromatogram reconstruction of highres data 
- 
------------------------------------------------------------------------- 
-r4758 | eng_jk | 2009-11-12 10:54:38 -0800 (Thu, 12 Nov 2009) | 2 lines 
- 
-get rid of unnecessary backslashes in the sed command 
- 
------------------------------------------------------------------------- 
-r4757 | eng_jk | 2009-11-12 10:27:38 -0800 (Thu, 12 Nov 2009) | 2 lines 
- 
-escape ', ", & and replace <, > with [, ] respectively in the def lines 
- 
------------------------------------------------------------------------- 
-r4730 | eng_jk | 2009-10-30 11:03:06 -0700 (Fri, 30 Oct 2009) | 2 lines 
- 
-add maximum charge output option; get rid of incorrect hydrogen mass option for charge calculation 
- 
------------------------------------------------------------------------- 
-r4623 | eng_jk | 2009-09-16 09:13:05 -0700 (Wed, 16 Sep 2009) | 2 lines 
- 
-[subsetdb] add -D option for user specified reverse description prefix 
- 
------------------------------------------------------------------------- 
-r4619 | eng_jk | 2009-09-14 11:55:15 -0700 (Mon, 14 Sep 2009) | 2 lines 
- 
-add 2 more digits of precision for expect score output 
- 
------------------------------------------------------------------------- 
-r4617 | eng_jk | 2009-09-09 15:03:24 -0700 (Wed, 09 Sep 2009) | 2 lines 
- 
-[Out2XML] modify parsing of .out files with duplicate references 
- 
------------------------------------------------------------------------- 
-r4595 | eng_jk | 2009-08-27 14:06:37 -0700 (Thu, 27 Aug 2009) | 2 lines 
- 
-[comet-fastadb.cgi] update URLs 
- 
------------------------------------------------------------------------- 
-r4594 | eng_jk | 2009-08-27 13:06:11 -0700 (Thu, 27 Aug 2009) | 2 lines 
- 
-[ProteinProphet] deal with missing description lines for IPI database searches 
- 
------------------------------------------------------------------------- 
-r4593 | eng_jk | 2009-08-26 14:48:55 -0700 (Wed, 26 Aug 2009) | 2 lines 
- 
-[XPRESS] add chromatogram minimum ion count for a peptide to be quantified; -c<num> option with default value of 5. The goal is to avoid calculating areas/ratios for spurious peaks (those with fewer than 5 MS1 scan signals contributing to elution area calculation). 
- 
------------------------------------------------------------------------- 
-r4592 | eng_jk | 2009-08-26 14:26:50 -0700 (Wed, 26 Aug 2009) | 2 lines 
- 
-[readmzXML] add precursorCharge to -H output 
- 
------------------------------------------------------------------------- 
-r4591 | eng_jk | 2009-08-26 13:16:33 -0700 (Wed, 26 Aug 2009) | 2 lines 
- 
-[XPressCGIProteinDisplayParser.cgi] a counter/index variable was re-used in an inner loop causing outer loop to exit prematurely resulting in the CGI not displaying peptide ratios from all input files; problem appears to be present in initial commit 
- 
------------------------------------------------------------------------- 
-r4589 | eng_jk | 2009-08-26 11:42:00 -0700 (Wed, 26 Aug 2009) | 2 lines 
- 
-[XPRESS] fix bug that causes N15 metabolic labeling option to run incorrectly (introduced when C13 option added) 
- 
------------------------------------------------------------------------- 
-r4585 | eng_jk | 2009-08-20 11:48:05 -0700 (Thu, 20 Aug 2009) | 2 lines 
- 
-[psm2pdf] add e-value score cutoff option (versus PP probability) and clean up 
- 
------------------------------------------------------------------------- 
-r4576 | eng_jk | 2009-08-18 11:20:12 -0700 (Tue, 18 Aug 2009) | 2 lines 
- 
-[psm2pdf] Initial add of program that generates a pdf of annotated spectra from input interact.pep.xml files. Requires htmldoc and ghostscript. 
- 
------------------------------------------------------------------------- 
-r4575 | eng_jk | 2009-08-18 11:15:11 -0700 (Tue, 18 Aug 2009) | 2 lines 
- 
-[psm2pdf] create source directory 
- 
------------------------------------------------------------------------- 
-r4574 | eng_jk | 2009-08-14 10:23:19 -0700 (Fri, 14 Aug 2009) | 2 lines 
- 
-[plot-msms] modifications to support bulk image generation for publication 
- 
------------------------------------------------------------------------- 
-r4536 | eng_jk | 2009-08-06 16:56:19 -0700 (Thu, 06 Aug 2009) | 2 lines 
- 
-[Out2XML] address negative deltacnstar values that were being reported. 
- 
------------------------------------------------------------------------- 
-r4534 | eng_jk | 2009-08-06 16:35:15 -0700 (Thu, 06 Aug 2009) | 2 lines 
- 
-[Out2XML] Set deltacnstar to 0.001 when xcorr of top 2 homologous peptides are exactly the same; fixes current behavior (since rev 3913) which would have this attribute value be set to 0.0 under this scenario. Retention time is retrieved from start_scan whereas code before would grab from end_scan; those scan numbers are the same in our pipeline. Print more precision for spscore for UW version of Sequest that replaces spsore with e-value. 
- 
------------------------------------------------------------------------- 
=== zhisun === === zhisun ===

Revision as of 18:18, 4 August 2010

To developers: I put this page in place to help manage the 4.4.0 "Vuvuzela" release. The punch list is a list of tasks/issues that need to be resolved for the list. I'll incorporate the known issues and the release notes into the final release bulletin. To facilitate the generation of the release notes I've captured all of the subversion change logs and sorted them by user. Please review your set of changes condense them into what you want to say about the changes for the release.

Contents

Punch List

  • Remove ReadW.exe, trapper, and mzWiff from build
  • investigate larger size of Windows installer, grew from 63MB to a whopping 176MB
    • turns out to be MaRiMba spectral libraries included in build. Checking to see if these are needed
  • include details from Eric's old email
  • Change installer to look for 64 bit ActiveState perl

Known issues

  • XPressPeptideParser crash 
>> When Brian
>> was working through testing for Chris P's code review, he had some
>> issues (unrelated to Chris) that showed some trunk issues.
Yeah, specifically what I found was that starting with Jimmy's change
4785 I get a crash in XPressPeptideParser with one of my smoketest
data sets, but only on my MinGW build (not MSVC, not linux), and not
in gdb (that last detail says "stack issue" to me).  Looking at the
changes in that commit I don't think it's anything Jimmy did, I think
that just happened to expose a latent stack issue which I've had no
luck tracking down.
>> Given that nobody else seems to have hit this I think we should just
>> let it ride.
Sorry, I meant 4782.  When I roll back to 4781 I don't get a crash,
when I go to 4782 I do.  But again, I can't see that it's anything you
did in that commit, and I can't repro inside gdb, or with MSVC under
any circumstance.

Brian

Release Notes

Trunk changes since revision 4498 (creation of 4.3 branch by spacepod)

cpaulse

r4974 | cpaulse | 2010-05-13 12:13:21 -0700 (Thu, 13 May 2010) | 1 line

fix tpp.sln for vc9

r4918 | cpaulse | 2010-03-29 14:33:30 -0700 (Mon, 29 Mar 2010) | 5 lines

Branch visual studio 8 tpp.sln file (and dependent vcproj files) to tppvc8.sln.

tpp.sln and dependent vcproj files converted to visual studio 2008 express, with atl/mfc dependent projects (mzwiff, trapper, masswolf, readw), msconvert, and pwiz_swig projects removed from tpp.sln (last two don't compile in 2008 express and have no internal dependencies). extern/build_boost_vc8.bat renamed.

minor bug fix to release configuration of readmzXML.vcproj.

r4917 | cpaulse | 2010-03-29 11:08:10 -0700 (Mon, 29 Mar 2010) | 2 lines

Fix reading of search engine specific input data where multiple search results are present for a single spectrum. Compile warning in Visual C++ (PhosphoMixtureDistr.cxx).

r4901 | cpaulse | 2010-03-12 08:51:32 -0800 (Fri, 12 Mar 2010) | 1 line

fix destructor semantics for iProphet

r4899 | cpaulse | 2010-03-10 12:04:17 -0800 (Wed, 10 Mar 2010) | 1 line

don't delete RT and PI mixtureDistr's twice.

r4898 | cpaulse | 2010-03-10 09:13:32 -0800 (Wed, 10 Mar 2010) | 1 line

fix memory leaks in PeptideProphetParser, and type cast warnings generated by visual studio in spectrast

r4890 | cpaulse | 2010-02-28 14:32:24 -0800 (Sun, 28 Feb 2010) | 1 line

undo my destruction of Peptide::mods semantics.

r4889 | cpaulse | 2010-02-26 11:35:58 -0800 (Fri, 26 Feb 2010) | 1 line

more missed files intended for changeset 4885

r4887 | cpaulse | 2010-02-26 11:19:01 -0800 (Fri, 26 Feb 2010) | 1 line

missed from changeset 4885

r4885 | cpaulse | 2010-02-25 15:21:11 -0800 (Thu, 25 Feb 2010) | 1 line

modernize integer definitions enough to stop visual studio 9 from issuing warnings at level 3.

real_procopio

pepXML schema

  • New pepXML 1.15: Adds more search engines (ProteinPilot, ProteinLynx, Spectrum Mill, greylag, Phenyx, Proteios, Crux, Tide) and activation methods (ETD/CID, HCD).


MzXML2Search

  • Added "mzML" to usage statement


Petunia

  • Moved mzXML utils to new tab
  • Changed wording on home page to state using mzML as the standard
  • Added indexmzXML page
  • Optionally authenticate against an .htpasswd entry (from J.Slagel)
  • Fix tabs (from 4.3 branch)

New options

  • PeptideProphet:
    • Use Phospho model
  • XPRESS:
    • Allow passing of negative mass offsets
    • Min Points needed
    • Sum N isotopic peaks)
  • MzXML2Search:
    • Output N Top Peaks
    • Max Charge State
    • Output Precision
    • Removed ion mass option

Technical changes:

  • Minor corrections to session handling
  • Add trailing slash to tppbin definition
  • Added a variable to hold location of tpp-bin
  • Refer to tpp_hostname by full path
  • Silence perl warning (more to go...)
  • Provide path to plotspectrast.cgi when calling Lib2HTML
  • Minor form closing changes to avoid mis-formatting in IE


xinteract

  • Adding isotopic peaks XPRESS option to usage statement


readmzXML

  • Add -r option to output spectrum data only; no title or extra CR's. (Replicates functionality of Jimmy's getSpectrum)


Pep3D

  • Enable viewing of MS2-only data (no elution, but at least you can see the distribution of sequencing events)
  • Larger input field for filename
  • Use dhtml to print/display messages (also simplify error messages so they display correctly).


plot-msms (spectrum viewer)

  • Added Image Size option
  • Update to unified look and feel


protxml2html (ProteinProphet viewer)

  • Add command-line usage statement
  • Took out a bunch of commented-out code.
  • Performance improvements:
    • Define several 'global' variables in xsl to avoid costly lookups
    • Add option not to generate Gaggle files

Limited testing gives speeds up to 5x faster than previous version.

dctrud

r4884 | dctrud | 2010-02-25 02:42:00 -0800 (Thu, 25 Feb 2010) | 1 line

[ASAPRatioProteinRatioParser] Implement PepXML cacheing as XPRESS

pcbrefugee

r5043 | pcbrefugee | 2010-06-24 08:22:26 -0700 (Thu, 24 Jun 2010) | 1 line

[Mascot2XML] fatal error messages about enzyme definition issues are always useful, ignore the state of verbose_ flag for these

r5036 | pcbrefugee | 2010-06-14 16:16:26 -0700 (Mon, 14 Jun 2010) | 1 line

[pwiz] sync up to latest from ProteoWizard, their rev 2047

r4995 | pcbrefugee | 2010-05-28 10:56:11 -0700 (Fri, 28 May 2010) | 1 line

[pwiz] get current with ProteoWizard codebase - sync to pwiz commit number 2005

r4992 | pcbrefugee | 2010-05-28 10:21:54 -0700 (Fri, 28 May 2010) | 1 line

[indexmzXML] light changes to accomodate ever-stricter GCC's handling of long long (it doesn't like that), also fix and off-by-one error that left the last entry in the index untested.

r4954 | pcbrefugee | 2010-04-20 13:12:51 -0700 (Tue, 20 Apr 2010) | 1 line

[various] add a bunch of missing initializations - stack and dynamically allocated memory cannot be expected to be zeroed out. Also, don't call delete on malloc'd memory, use free instead.

r4937 | pcbrefugee | 2010-04-09 17:03:15 -0700 (Fri, 09 Apr 2010) | 1 line

[MzXMLSearch] change a variable size stack allocation of peak structs to new/delete allocation (some older compilers don't like that syntax, and it risks stack overflow too)

r4935 | pcbrefugee | 2010-04-09 15:39:07 -0700 (Fri, 09 Apr 2010) | 1 line

[MzXML2Search] fix a crash when WEBSERVER_ROOT env variable isn't set

r4929 | pcbrefugee | 2010-04-06 12:50:50 -0700 (Tue, 06 Apr 2010) | 1 line

[Pepc] update GWT and GChart to current versions and tweak color select code to satisfy IE8

r4928 | pcbrefugee | 2010-04-05 15:07:46 -0700 (Mon, 05 Apr 2010) | 1 line

[pwiz] add a missing pwiz source file for ABI_T2D that was tripping up the xtandem build on linux

r4926 | pcbrefugee | 2010-04-01 10:28:53 -0700 (Thu, 01 Apr 2010) | 1 line

[pwiz] handful of pwiz files missed again(!) in the previous commit (something's up with my TortoiseSVN installation?)

r4925 | pcbrefugee | 2010-04-01 09:59:20 -0700 (Thu, 01 Apr 2010) | 1 line

[pwiz] handful of pwiz files missed in the previous commit

r4924 | pcbrefugee | 2010-04-01 08:34:04 -0700 (Thu, 01 Apr 2010) | 1 line

synch up to Proteowizard rev 1925

r4920 | pcbrefugee | 2010-03-30 16:11:50 -0700 (Tue, 30 Mar 2010) | 1 line

Finish various renames of VC8 project files for the VC8 build.

r4919 | pcbrefugee | 2010-03-30 15:57:47 -0700 (Tue, 30 Mar 2010) | 1 line

tidy up notes to match current code

r4914 | pcbrefugee | 2010-03-23 16:15:51 -0700 (Tue, 23 Mar 2010) | 1 line

tweaks for MSVC build

r4913 | pcbrefugee | 2010-03-23 15:41:24 -0700 (Tue, 23 Mar 2010) | 1 line

[PepC] allow more seperator types in CSV files (comma, tab, semicolon, colon, space) and properly handle error cases where none of those are present. Also tweak IntelliJ project file to be directory location independent.

r4912 | pcbrefugee | 2010-03-22 15:47:43 -0700 (Mon, 22 Mar 2010) | 1 line

adding externals for rebuilding PepC jar file

r4911 | pcbrefugee | 2010-03-22 14:19:40 -0700 (Mon, 22 Mar 2010) | 1 line

integrate PepC statistical peptide counting into TPP GUI (commandline version was added in commit 4886). Somewhat underdocumented at the moment, will add link to accompanying paper as soon as it becomes available.

r4888 | pcbrefugee | 2010-02-26 11:34:57 -0800 (Fri, 26 Feb 2010) | 1 line

[PepC] - some documentation tweaks

r4886 | pcbrefugee | 2010-02-25 15:58:56 -0800 (Thu, 25 Feb 2010) | 1 line

initial commit of "PepC: Proteomics software for identifying differentially expressed proteins based on spectral counting." developed by Insilicos with Lev Becker et al at the UW Heinecke lab (paper has been submitted to Bioinformatics). Changes for integration with Petunia will come in a different commit - what's here is sufficient for commandline usage.

r4877 | pcbrefugee | 2010-02-22 08:46:38 -0800 (Mon, 22 Feb 2010) | 1 line

properly escape FASTA protein descriptions containing reserved XML characters in pepXML output

r4856 | pcbrefugee | 2010-01-15 17:01:37 -0800 (Fri, 15 Jan 2010) | 1 line

[ProteoWizard] a handful more missed commits from recent ProteoWizard code reorg

r4855 | pcbrefugee | 2010-01-15 16:12:00 -0800 (Fri, 15 Jan 2010) | 1 line

[ProteoWizard] add a few things I missed from the most recent ProteoWizard code tree reorganization, update to ProteoWizard rev 1707

r4854 | pcbrefugee | 2010-01-15 14:44:15 -0800 (Fri, 15 Jan 2010) | 1 line

[proteowizard] sync up with proteowizard rev 1699, which includes my fix for reading mzXML files with nested scans (only affects TPP when reading mzXML without newlines, in which case RAMP passes off to pwiz).

r4852 | pcbrefugee | 2010-01-15 13:25:47 -0800 (Fri, 15 Jan 2010) | 1 line

[xinteract] skip the iprophet stuff for LabKey purposes (currently internally identified as "non interactive mode", which becomes a misnomer now, since this has nothing to do with interactivity and is a more general config issue)

r4851 | pcbrefugee | 2010-01-15 13:23:17 -0800 (Fri, 15 Jan 2010) | 1 line

[xtandem] No functional change, just a couple of standard include file adds/drops for crossplatform purposes, and identify the build as our own variant: VERSION "2009.10.01.1 (LabKey and ISB) " instead of just "2009.10.01.1".

r4814 | pcbrefugee | 2010-01-11 11:46:52 -0800 (Mon, 11 Jan 2010) | 1 line

[tpp_gui/win32] consistent use of single quotes so perl_paths build step can find and replace /usr/bin with windowsy default path

r4795 | pcbrefugee | 2009-12-14 08:38:47 -0800 (Mon, 14 Dec 2009) | 1 line

[mzXML] a copy of http://sashimi.sourceforge.net/schema_revision/mzXML_3.0/mzXML_3.0.xsd for convenience, it's surprisingly difficult to locate online if you don't know where to look already

r4793 | pcbrefugee | 2009-12-10 17:45:24 -0800 (Thu, 10 Dec 2009) | 1 line

[pwiz] silence some gcc 4.2.4 warnings about assigning string constant to non-const char *

r4792 | pcbrefugee | 2009-12-10 16:20:39 -0800 (Thu, 10 Dec 2009) | 1 line

[pwiz mzML reader code] sync up with ProteoWizard project at their rev 1608, for mzML CV version 2.29.0. Missed a handful of adds in previous commit.

r4790 | pcbrefugee | 2009-12-10 15:54:38 -0800 (Thu, 10 Dec 2009) | 1 line

[pwiz mzML reader code] sync up with ProteoWizard project at their rev 1608, for mzML CV version 2.29.0. Changes are not a drastic as length of commit list might seem to imply, much of that is just changes in header comments due to an author's change of institution

r4789 | pcbrefugee | 2009-12-10 12:18:32 -0800 (Thu, 10 Dec 2009) | 1 line

[ASAPRatio CGI] don't mistake "cidIndx" for "Indx" while parsing html field values, per user dctrud in https://mail.google.com/a/insilicos.com/#label/spctools-discuss/125795e322f2433b

r4788 | pcbrefugee | 2009-12-09 16:46:10 -0800 (Wed, 09 Dec 2009) | 1 line

[pwiz] tidy up the MSVC build for pwiz JNI bindings (no more win_lib), add a clean-pwiz_swig target to Makefile.pwiz.incl

r4787 | pcbrefugee | 2009-12-04 16:59:09 -0800 (Fri, 04 Dec 2009) | 1 line

[pwiz] create the java bindings output directory if need be

r4786 | pcbrefugee | 2009-12-04 16:54:12 -0800 (Fri, 04 Dec 2009) | 1 line

[pwiz] add an optional target "pwiz_swig" to generate JNI wrappers for pwiz's RAMPAdapter. Not actually used by TPP, but useful for other projects that use TPP components.

r4781 | pcbrefugee | 2009-11-24 09:28:39 -0800 (Tue, 24 Nov 2009) | 1 line

[MzXML2Search] tweak the usage statement, "-T" sets maximum MH+ mass, not "maximum MH+ scan".

r4780 | pcbrefugee | 2009-11-23 09:23:25 -0800 (Mon, 23 Nov 2009) | 1 line

[ProteinProphet] call to writeErrorAndSens is still needed even when running non-interactively, as in LabKey Server usage

r4776 | pcbrefugee | 2009-11-17 14:27:00 -0800 (Tue, 17 Nov 2009) | 1 line

[out2xml] add a cast (int)strlen for quiet compile

r4774 | pcbrefugee | 2009-11-16 11:58:31 -0800 (Mon, 16 Nov 2009) | 1 line

[xtandem] remove an unneeded (and, to some compilers, offensive) class declaration within class definition of the same

r4773 | pcbrefugee | 2009-11-16 10:36:32 -0800 (Mon, 16 Nov 2009) | 1 line

[windows build] tweak the readme to remove references to win_lib

r4761 | pcbrefugee | 2009-11-12 15:05:48 -0800 (Thu, 12 Nov 2009) | 32 lines

[xtandem] updates from labkey guys to get us at least partly up to date with GPM - see attachment in my email to spctools-dev of Nov 12 2009, the crucial part of which is copied here with total loss of formatting:

2. Details 2.1 Make TPP fork current (jeckels)


Item Change Justification 2.1.A mscore.cpp To mimic SEQUEST-like scoring, a scoring plugin has to modify the theoretical fragment ion series to adjust intensities and add appropriate neutral losses. To allow this make mscore::load_seq virtual under #ifdef PLUGGABLE_SCORING


2.2 Consider merging additional changes from GPM tree into TPP fork (jeckels) These are the changes in the current GPM sources that seem unrelated to our changes and relatively useful.

Item Change Justification

2.2.a tandem.cpp p3.cpp Current source code in the GPM has implements a round-robin allocation of work to threads that results in better balance of execution time between threads. Requested by Matt Fitzgibbon. Note the 2 files are almost identical, they compile under different flags

2.2.b mscore.cpp , GPM version at lines 530 and 1573 Current GPM builds have added support for including doubly charged y-ions in the scoring. This will raise some scores to make them more accurate. Requested by Matt Fitzgibbon.

2.2.c mscore.cpp Other changes in the GPM appear to be for compiler issues. E.g. surrounding a float literal with parenthesis. If we take all the changes in GPMs version the only different that remains will be the change from 2.1.A above.

2.2.d mpmods.cpp mprocess.cpp msequtilities.cpp GPM ads support for annotation files for enumerating possible mods Tags are refine, use annotations protein, use annotations GPM defaults to yes on both but we could default to no

2.2.e mscorepam.h GPM's mscorepam.h has a change with comment "WCH: wrong pair attribute checking"


r4751 | pcbrefugee | 2009-11-11 16:22:13 -0800 (Wed, 11 Nov 2009) | 1 line

[xinteract] when creating or running regression tests, ignore the WEBSERVER_TMP environment variable - tempfile use and the temporary renames that come with it whacks out the regression test files.

r4634 | pcbrefugee | 2009-09-23 14:49:57 -0700 (Wed, 23 Sep 2009) | 1 line

[installers] hunt down and remove any manual steps required to get all new and former pepXML and protXML schemas into the windows installer, and the *nix "make install"

r4625 | pcbrefugee | 2009-09-18 11:10:33 -0700 (Fri, 18 Sep 2009) | 1 line

[ProteinProphet] more informative error message when pepXML simply contains no analyses from peptideProphet (or interProphet, as appropriate)

r4618 | pcbrefugee | 2009-09-11 11:27:03 -0700 (Fri, 11 Sep 2009) | 1 line

[Mascot2XML] handle yet another title variant, example: "title=spectrumId=3774 Polarity=Positive ScanMode=MassScan TimeInSeconds=3710.73"

r4597 | pcbrefugee | 2009-08-31 14:11:34 -0700 (Mon, 31 Aug 2009) | 1 line

[xtandem / mzML 1.0 backward compatibility] - tweaks to pwiz RAMPAdapter to handle mzML 1.0 description of precursor ions

r4583 | pcbrefugee | 2009-08-18 17:50:33 -0700 (Tue, 18 Aug 2009) | 1 line

[plot-msms] deal with a signed/unsigned warning (with a probably unmeasurable performance improvement)

r4581 | pcbrefugee | 2009-08-18 17:20:33 -0700 (Tue, 18 Aug 2009) | 1 line

[xtandem] tandem's custom mzXML parser wasn't expecting compressionType="none"

r4580 | pcbrefugee | 2009-08-18 17:01:17 -0700 (Tue, 18 Aug 2009) | 1 line

[mzML reading] get current with pwiz 1.6 branch to fix a problem with reading WIFF-originated mzML files (was throwing an exception due to complicated nativeID, now we just use the index as scan number instead)

r4579 | pcbrefugee | 2009-08-18 13:11:08 -0700 (Tue, 18 Aug 2009) | 1 line

[amazon ec2 builds] add ubuntu 9.10 as a supported OS, using the 9.04 config scripts

r4578 | pcbrefugee | 2009-08-18 13:00:41 -0700 (Tue, 18 Aug 2009) | 1 line

[xtandem] tweak for building under GCC 4.4.0 (including fake stdint.h for win32 builds)

r4577 | pcbrefugee | 2009-08-18 12:25:21 -0700 (Tue, 18 Aug 2009) | 1 line

[perl scripts] use $FindBin::Bin to locate tpp_hostname executable

r4529 | pcbrefugee | 2009-08-05 15:08:55 -0700 (Wed, 05 Aug 2009) | 1 line

[indexmzXML] add this tool to the standard install, use RAMP interface to get 64 bit file pointers for proper indexing on win32

r4517 | pcbrefugee | 2009-08-04 14:07:39 -0700 (Tue, 04 Aug 2009) | 1 line

[pwiz build] add a couple of files which our use of RAMPAdapter doesn't actually require, but which are missed by some library managers as unresolved references

r4514 | pcbrefugee | 2009-08-04 10:00:35 -0700 (Tue, 04 Aug 2009) | 1 line

[mzML handling] cutting over to latest ProteoWizard code, to pick up mzML 1.1 capability (including mzML 1.0 read capability)

r4511 | pcbrefugee | 2009-08-03 13:36:34 -0700 (Mon, 03 Aug 2009) | 1 line

[fileDownloader.pl] tweak to make this compatible with the win32-specific perl_paths make step that removes hardcoded /usr/bin path to wget etc - no effect on linux usage

r4510 | pcbrefugee | 2009-08-03 12:55:41 -0700 (Mon, 03 Aug 2009) | 1 line

[mzML handling] update ProteoWizard external references to rev 1132, to include changes for mzML 1.0 read capability

r4508 | pcbrefugee | 2009-08-02 16:46:39 -0700 (Sun, 02 Aug 2009) | 1 line

[petunia] on win32, prepend full install path to commands (should help with .pl files as commands, which the win32 path mechanism doesn't know to search for)

r4502 | pcbrefugee | 2009-07-30 14:53:56 -0700 (Thu, 30 Jul 2009) | 1 line

[win32 installer] temp rename of README to README.txt while building installer allows windows to know how to display the readme doc at install time. Already did this for the MSVC installer build process, forgot about mingw.

ppatrick

r4850 | ppatrick | 2010-01-15 09:30:24 -0800 (Fri, 15 Jan 2010) | 1 line

Fixed basePeak m/z and intensity bug for centroided data.

dshteyn

r5035 | dshteyn | 2010-06-11 16:23:04 -0700 (Fri, 11 Jun 2010) | 1 line

Removing debugging output

r5032 | dshteyn | 2010-06-10 10:26:29 -0700 (Thu, 10 Jun 2010) | 1 line

Make sure there are enough bits.

r5028 | dshteyn | 2010-06-09 11:13:33 -0700 (Wed, 09 Jun 2010) | 1 line

RTCalc: copy coefficients file to staging area.

r5027 | dshteyn | 2010-06-08 10:22:06 -0700 (Tue, 08 Jun 2010) | 1 line

Adding RTCalc to list of executables to build

r5026 | dshteyn | 2010-06-07 14:18:24 -0700 (Mon, 07 Jun 2010) | 1 line

RTCalc: fix memory leak.

r5025 | dshteyn | 2010-06-07 11:33:34 -0700 (Mon, 07 Jun 2010) | 1 line

Fix install of RTCalc under linux.

r5024 | dshteyn | 2010-06-04 11:54:40 -0700 (Fri, 04 Jun 2010) | 1 line

Remove source control directories after the PepcView copy.

r5023 | dshteyn | 2010-06-04 11:27:02 -0700 (Fri, 04 Jun 2010) | 1 line

Out2XML: Use all of the last part of the encoded spectrum name for the charge not just one character, for multi character charge states

r5022 | dshteyn | 2010-06-04 11:05:43 -0700 (Fri, 04 Jun 2010) | 1 line

Changes to get Pepc to install

r5021 | dshteyn | 2010-06-04 10:40:48 -0700 (Fri, 04 Jun 2010) | 1 line

RTCalc switch from size_t to int since value is initialized to -1

r5020 | dshteyn | 2010-06-03 12:05:33 -0700 (Thu, 03 Jun 2010) | 1 line

Installing RTCalc and coefficients.

r5019 | dshteyn | 2010-06-03 12:04:59 -0700 (Thu, 03 Jun 2010) | 1 line

Default coefficients.

r5018 | dshteyn | 2010-06-03 12:03:45 -0700 (Thu, 03 Jun 2010) | 1 line

Replace hard paths.

r5017 | dshteyn | 2010-06-02 12:57:19 -0700 (Wed, 02 Jun 2010) | 1 line

PepXMLViewer: Display only top ranked search_hit. Populate fields with search scores from any of the engines used in the analysis (useful for iProphet viewing).

r5016 | dshteyn | 2010-06-02 12:52:13 -0700 (Wed, 02 Jun 2010) | 1 line

ASAPRatio: changes to display ratios of secondary proteins from protein groups. TODO: Next and Prev Protein buttons will take you to the next protein group not the next protein in the group, should be corrected or disabled.

r5015 | dshteyn | 2010-06-02 12:46:59 -0700 (Wed, 02 Jun 2010) | 1 line

PeptideProphetParser: Replace SSRCalc with RTCalc for retention time modelling.

r5014 | dshteyn | 2010-06-02 12:45:51 -0700 (Wed, 02 Jun 2010) | 1 line

PeptideProphetParser: Replace SSRCalc with RTCalc for retention time modelling.

r5013 | dshteyn | 2010-06-02 12:44:37 -0700 (Wed, 02 Jun 2010) | 1 line

PeptideProphetParser: Add writing of .RTcoeff file for RT modeling

r5012 | dshteyn | 2010-06-02 12:40:18 -0700 (Wed, 02 Jun 2010) | 1 line

RefreshParser: Only map unrejected peptides.

r5011 | dshteyn | 2010-06-02 12:38:25 -0700 (Wed, 02 Jun 2010) | 1 line

Store modified_peptide separately for RT calculation

r5010 | dshteyn | 2010-06-02 12:36:45 -0700 (Wed, 02 Jun 2010) | 1 line

RTCalc: New tool for replacing of SSRCalc in the TPP.

r5009 | dshteyn | 2010-06-02 12:35:27 -0700 (Wed, 02 Jun 2010) | 1 line

Add consts to unchanged input strings

r5008 | dshteyn | 2010-06-02 12:33:55 -0700 (Wed, 02 Jun 2010) | 1 line

Add consts to unchanged input strings

r5007 | dshteyn | 2010-06-02 12:32:44 -0700 (Wed, 02 Jun 2010) | 1 line

FANN and GSL build targets

r5006 | dshteyn | 2010-06-02 12:31:55 -0700 (Wed, 02 Jun 2010) | 1 line

FANN and GSL build targets

r5005 | dshteyn | 2010-06-02 12:28:54 -0700 (Wed, 02 Jun 2010) | 1 line

New libraries for RTCalc. Fast Artificial Neural Network (FANN). GNU Scientific Lib (GSL)

r5004 | dshteyn | 2010-06-02 12:24:03 -0700 (Wed, 02 Jun 2010) | 1 line

ASAPRatio: changes to display ratios of secondary proteins from protein groups.

r5002 | dshteyn | 2010-06-01 16:17:00 -0700 (Tue, 01 Jun 2010) | 1 line

Using ppm in the accurate mass model

r5001 | dshteyn | 2010-06-01 16:10:14 -0700 (Tue, 01 Jun 2010) | 1 line

PeptideProphetParser: New RT model.

r5000 | dshteyn | 2010-06-01 16:06:39 -0700 (Tue, 01 Jun 2010) | 1 line

PeptideProphetParser: Report error and don't model spectra with assumed_charge not equal to encoded charge in the name. Fix bug reported by Ludovic.

r4956 | dshteyn | 2010-04-21 11:15:56 -0700 (Wed, 21 Apr 2010) | 1 line

InteractParser: Make sure to not strip out the enzyme info when not specified on commandline.

r4934 | dshteyn | 2010-04-07 17:05:46 -0700 (Wed, 07 Apr 2010) | 1 line

InteractParser: BUGFIX prevent double delete of tag pointer.

r4927 | dshteyn | 2010-04-01 11:17:31 -0700 (Thu, 01 Apr 2010) | 1 line

InteractParser: Fix crash when -E option is not specified.

r4915 | dshteyn | 2010-03-24 16:51:31 -0700 (Wed, 24 Mar 2010) | 1 line

Tandem2XML: Handle multiple variable mods on same AA

r4882 | dshteyn | 2010-02-24 11:45:34 -0800 (Wed, 24 Feb 2010) | 1 line

InteractParser: fix my compilation bug.

r4881 | dshteyn | 2010-02-23 18:50:35 -0800 (Tue, 23 Feb 2010) | 1 line

Correct MINPROB option problem.

r4879 | dshteyn | 2010-02-23 16:18:00 -0800 (Tue, 23 Feb 2010) | 1 line

RefreshParser: report the prev_aa and next_aa for top NTT match in the protein, not just the first entry. Test that db defn line actually has a '|' before testing if it comes before a ' '.

r4878 | dshteyn | 2010-02-23 14:29:53 -0800 (Tue, 23 Feb 2010) | 1 line

InteractParser: When an enzyme is given on the commandline overwrite the current sample_enzyme tag with the enzyme specified, old behaviour introduced competing sample_enzyme tags creating an inconsistency under certain conditions of use.

r4875 | dshteyn | 2010-02-17 11:49:26 -0800 (Wed, 17 Feb 2010) | 1 line

InterProphetParser - better usage statement, new option to output only peptides above a certain probability value.

r4874 | dshteyn | 2010-02-17 11:46:22 -0800 (Wed, 17 Feb 2010) | 1 line

InterProphetParser - adding computation of observed fits among initially low and high probability results, using variable bandwidths from the modeled fits.

r4871 | dshteyn | 2010-02-10 15:48:48 -0800 (Wed, 10 Feb 2010) | 1 line

Undo last checkin.

r4870 | dshteyn | 2010-02-10 15:39:55 -0800 (Wed, 10 Feb 2010) | 1 line

Xpress refered to this value.

r4853 | dshteyn | 2010-01-15 14:03:41 -0800 (Fri, 15 Jan 2010) | 1 line

ProteinProphet Store a separate value with peptide's total weight in the protein group.

r4849 | dshteyn | 2010-01-14 14:36:03 -0800 (Thu, 14 Jan 2010) | 1 line

Switch to a more robust split statement.

r4848 | dshteyn | 2010-01-14 12:00:53 -0800 (Thu, 14 Jan 2010) | 1 line

Adding InspectFvalue, PHOSPHO model, TOPCAT model.

r4847 | dshteyn | 2010-01-14 11:55:41 -0800 (Thu, 14 Jan 2010) | 1 line

xinteract PHOSPHO model and enable option InteractParser -P for correcting protein names in omssa output.

r4846 | dshteyn | 2010-01-14 11:46:01 -0800 (Thu, 14 Jan 2010) | 1 line

PeptideProphetParser new PHOSPHO model. Check all matching proteins for a peptide and count it as decoy only if all are decoys. Tuning max reward parameters for ACCMASS model. Print warning if not decoys are found. Count decoys and forward PSMs found.

r4845 | dshteyn | 2010-01-14 11:45:21 -0800 (Thu, 14 Jan 2010) | 1 line

PeptideProphetParser new PHOSPHO model. Check all matching proteins for a peptide and count it as decoy only if all are decoys. Tuning max reward parameters for ACCMASS model. Print warning if not decoys are found.

r4844 | dshteyn | 2010-01-14 11:42:42 -0800 (Thu, 14 Jan 2010) | 1 line

PeptideProphetParser new PHOSPHO model.

r4843 | dshteyn | 2010-01-14 11:42:23 -0800 (Thu, 14 Jan 2010) | 1 line

PeptideProphetParser new PHOSPHO model.

r4842 | dshteyn | 2010-01-14 11:24:48 -0800 (Thu, 14 Jan 2010) | 1 line

PeptideProphetParser new PHOSPHO model.

r4841 | dshteyn | 2010-01-14 11:23:48 -0800 (Thu, 14 Jan 2010) | 1 line

PeptideProphetParser new PHOSPHO model. Also fix the output when there are multiple top_hits so the probability is reported with the top most hit.

r4840 | dshteyn | 2010-01-14 11:05:58 -0800 (Thu, 14 Jan 2010) | 1 line

InterProphetParser TOPCAT model.

r4839 | dshteyn | 2010-01-14 11:05:18 -0800 (Thu, 14 Jan 2010) | 1 line

InterProphetParser Compute and report observed distributions in addition to the modeled distributions already reported.

r4838 | dshteyn | 2010-01-14 11:04:38 -0800 (Thu, 14 Jan 2010) | 1 line

InterProphetParser TOPCAT model. Filter out any old iProphet results from the final output file.

r4837 | dshteyn | 2010-01-14 11:03:47 -0800 (Thu, 14 Jan 2010) | 1 line

InterProphetParser TOPCAT model.

r4836 | dshteyn | 2010-01-14 11:03:10 -0800 (Thu, 14 Jan 2010) | 1 line

InterProphetParser TOPCAT model.

r4835 | dshteyn | 2010-01-14 11:02:39 -0800 (Thu, 14 Jan 2010) | 1 line

InterProphetParser TOPCAT model.

r4834 | dshteyn | 2010-01-14 11:01:38 -0800 (Thu, 14 Jan 2010) | 1 line

InterProphetParser Compute and report observed distributions in addition to the modeled distributions already reported.

r4833 | dshteyn | 2010-01-14 10:48:56 -0800 (Thu, 14 Jan 2010) | 1 line

InterProphetParser TOPCAT model.

r4832 | dshteyn | 2010-01-14 10:46:27 -0800 (Thu, 14 Jan 2010) | 1 line

ProteinProphet store peptide group weight (sum of peptide's weight in the protein group) separatelly from peptide's weight in the protein.

r4831 | dshteyn | 2010-01-14 10:27:49 -0800 (Thu, 14 Jan 2010) | 1 line

PeptideProphetParser tuning params on Tandem's semi-parametric model

r4830 | dshteyn | 2010-01-14 10:23:10 -0800 (Thu, 14 Jan 2010) | 1 line

PeptideProphetParser Inspect f-value model.

r4829 | dshteyn | 2010-01-14 10:22:35 -0800 (Thu, 14 Jan 2010) | 1 line

PeptideProphetParser Inspect f-value model.

r4828 | dshteyn | 2010-01-14 10:22:08 -0800 (Thu, 14 Jan 2010) | 1 line

PeptideProphetParser Inspect f-value model.

r4827 | dshteyn | 2010-01-14 10:18:07 -0800 (Thu, 14 Jan 2010) | 1 line

PeptideProphetParser Inspect f-value model.

r4826 | dshteyn | 2010-01-14 10:02:25 -0800 (Thu, 14 Jan 2010) | 1 line

PeptideProphetParser adjusting Myrimatch f-value params.

r4825 | dshteyn | 2010-01-13 14:53:47 -0800 (Wed, 13 Jan 2010) | 1 line

PeptideProphetParser tweaking the discriminant function params for OMSSA analysis

r4824 | dshteyn | 2010-01-13 14:48:27 -0800 (Wed, 13 Jan 2010) | 1 line

PeptideProphetParser tweaking the discriminant function params for OMSSA analysis

r4823 | dshteyn | 2010-01-13 14:36:25 -0800 (Wed, 13 Jan 2010) | 1 line

Caching variable bandwidth for quicker runtime. New function varBWdensityFit now can also take an additional parameter of a pointer to a Fit object.

r4822 | dshteyn | 2010-01-13 14:35:13 -0800 (Wed, 13 Jan 2010) | 1 line

Caching variable bandwidth for quicker runtime. New function varBWdensityFit now can also take an additional parameter of a pointer to a Fit object.

r4821 | dshteyn | 2010-01-13 14:28:57 -0800 (Wed, 13 Jan 2010) | 1 line

Safer way to clean up

r4820 | dshteyn | 2010-01-13 12:06:44 -0800 (Wed, 13 Jan 2010) | 1 line

New option for enabling the PHOSPHO PeptideProphet model.

r4819 | dshteyn | 2010-01-13 11:59:37 -0800 (Wed, 13 Jan 2010) | 1 line

PeptideProphetParser now stores all proteins matched by a search result.

r4818 | dshteyn | 2010-01-13 11:27:39 -0800 (Wed, 13 Jan 2010) | 1 line

PeptideProphetParser now stores all proteins matched by a search result.

r4817 | dshteyn | 2010-01-13 11:24:10 -0800 (Wed, 13 Jan 2010) | 1 line

MascotResult parsing memory bug fix

r4791 | dshteyn | 2009-12-10 16:01:30 -0800 (Thu, 10 Dec 2009) | 1 line

ASAPRATIO: Bug Fix, wrong masses were being computed for charge 5+, now corrected.

r4775 | dshteyn | 2009-11-17 11:25:44 -0800 (Tue, 17 Nov 2009) | 1 line

ASAPCGIDisplay.cgi: BUG FIX Normalized Ratio was not getting displayed.

r4627 | dshteyn | 2009-09-21 16:39:51 -0700 (Mon, 21 Sep 2009) | 1 line

PeptideProphet: Fixing seg fault appearing in MALDI mode on PROBID results.

r4598 | dshteyn | 2009-09-01 10:18:32 -0700 (Tue, 01 Sep 2009) | 1 line

RefreshParser: Bug fix with UNMAPPED peptides not showing up UNMAPPED under some conditions. Use minimum number of enzymatic termini from the search_hit num_tol_term attribute.

r4528 | dshteyn | 2009-08-05 15:04:15 -0700 (Wed, 05 Aug 2009) | 1 line

[ProteinProphet] Fix bug of indistinguishable_peptides being reported wrong with bad charge and first 2 chars stripped off.

r4519 | dshteyn | 2009-08-04 16:15:31 -0700 (Tue, 04 Aug 2009) | 1 line

[PeptideProphetParser] Make tool more robust by auto trimming whitespace from spectrum names. Tandem searches submitted by Scott Stansfield (Aug 2009) where generated with method mzXML->mgf->tandem->pepXML was adding an extra space to the end of spectrum name. This commit addresses the issue with Scott's data.

r4509 | dshteyn | 2009-08-03 12:26:22 -0700 (Mon, 03 Aug 2009) | 1 line

[InteractParser] Fix seg fault bug when dbtype option is set -T

henrylam

r5047 | henrylam | 2010-07-06 19:34:51 -0700 (Tue, 06 Jul 2010) | 1 line

[SpectraST] Add APPEND combineAction. Unhide several create options available in version 4.0

r5046 | henrylam | 2010-07-06 19:05:32 -0700 (Tue, 06 Jul 2010) | 1 line

[SpectraST] Change treatment of warnings. PepXMLImport will raise warning when pepXML file has no probabilities.

r5045 | henrylam | 2010-07-06 18:52:02 -0700 (Tue, 06 Jul 2010) | 1 line

[SpectraST] Compute NTT even if prev_aa or next_aa is X (treated as non-K,R,P)

r5042 | henrylam | 2010-06-20 02:37:35 -0700 (Sun, 20 Jun 2010) | 1 line

[SpectraST] Modernize library statistics reporting in pepidx: higher charges, more modifications, etc

r5041 | henrylam | 2010-06-19 09:18:57 -0700 (Sat, 19 Jun 2010) | 1 line

[SpectraST] Add two new search options: -sz (search all charge) and -s_FDL (specify fraction of delta in f-value)

r5040 | henrylam | 2010-06-19 08:49:53 -0700 (Sat, 19 Jun 2010) | 1 line

[SpectraST] Print sample info when protein is not available for xls and txt search output, good for non-peptide entries

r5039 | henrylam | 2010-06-19 08:29:53 -0700 (Sat, 19 Jun 2010) | 1 line

[SpectraST] -c_DTA option: Print first line without leading space to satisfy dta2mzxml

r5038 | henrylam | 2010-06-18 20:06:51 -0700 (Fri, 18 Jun 2010) | 1 line

[RTCalc] Catch return value of tpplib_system() to fix compiling warning/error on g++ 4.4.1 (Ubuntu 8.04)

r5037 | henrylam | 2010-06-18 20:00:50 -0700 (Fri, 18 Jun 2010) | 1 line

[SpectraST] Add Lib2HTML option to display entries sorted by precursor m/z

r4953 | henrylam | 2010-04-20 02:51:16 -0700 (Tue, 20 Apr 2010) | 1 line

[SpectraST] Parse and store collision energy information with library spectrum; Add code to keep or delete both of conflicting IDs for same spectrum (commented out for now)

r4951 | henrylam | 2010-04-16 00:38:37 -0700 (Fri, 16 Apr 2010) | 1 line

[ProphetModels.pl] Fix regex error when parsing newer iProphet pepXML files with neg_obs_dens and pos_obs_dens fields

r4950 | henrylam | 2010-04-16 00:31:26 -0700 (Fri, 16 Apr 2010) | 1 line

[calctppstat.pl] Options to specify probability or FDR threshold, to count number of unique proteins mapped to by PSMs

r4949 | henrylam | 2010-04-16 00:23:03 -0700 (Fri, 16 Apr 2010) | 1 line

[PeptideProphet] Printing error_point elements for lower (<1%) FDR thresholds

r4948 | henrylam | 2010-04-16 00:22:14 -0700 (Fri, 16 Apr 2010) | 1 line

[iProphet] Printing error_point elements for lower (<1%) FDR thresholds

r4947 | henrylam | 2010-04-16 00:08:36 -0700 (Fri, 16 Apr 2010) | 1 line

[xinteract] Allow specification of protein database for RefreshParser(and indirectly for ProteinProphet) by -D option (in case that information is not in the pepXML file). Skip RefreshParser, rather than quitting, if the database is not specified or not found.

r4946 | henrylam | 2010-04-15 23:52:57 -0700 (Thu, 15 Apr 2010) | 1 line

[ProteinProphet] Add NOPROTLEN option (now that PROTLEN is true by default); Continue execution even if protein database file is not specified or not present at the specified path.

r4892 | henrylam | 2010-03-02 03:06:21 -0800 (Tue, 02 Mar 2010) | 1 line

[SpectraST] Replace size_t with abstract types - undoing changes in r4885 - and add explicit casts (hopefully enabling smooth compilation on MSVS)

r4891 | henrylam | 2010-03-02 02:59:13 -0800 (Tue, 02 Mar 2010) | 1 line

[SpectraST] Fix msp import bug for M(O) containing peptides (bug introduced in r4815 on Jan12, 2010)

r4868 | henrylam | 2010-02-09 17:23:14 -0800 (Tue, 09 Feb 2010) | 1 line

[SpectraST] Change meaning of C[177] from Propionamide:2H(3) to Propionamide:13C(3)

r4867 | henrylam | 2010-02-09 01:56:10 -0800 (Tue, 09 Feb 2010) | 1 line

[SpectraST] Improved annotation algorithm

r4866 | henrylam | 2010-02-04 00:51:58 -0800 (Thu, 04 Feb 2010) | 1 line

[SpectraST] Fix naming errors when searching .gz files

r4865 | henrylam | 2010-02-01 18:15:41 -0800 (Mon, 01 Feb 2010) | 1 line

[SpectraST] PepXML import can now use all RAMP-supported types, including .gz

r4863 | henrylam | 2010-01-26 18:13:16 -0800 (Tue, 26 Jan 2010) | 1 line

[SpectraST] Minor fix of precursor neutral mass calculation in pepXML search output -- use mono or ave proton mass as appropriate

r4859 | henrylam | 2010-01-18 22:22:36 -0800 (Mon, 18 Jan 2010) | 1 line

[SpectraST] Change version number to 4.0

r4858 | henrylam | 2010-01-18 21:14:08 -0800 (Mon, 18 Jan 2010) | 1 line

[SpectraST] Semi-empirical spectra generation based on suer-specified modifications (beta). Evaluate phosphosite assignment (alpha - hidden option for now).

r4857 | henrylam | 2010-01-17 22:40:53 -0800 (Sun, 17 Jan 2010) | 1 line

[xinteract] Pass user-specified decoy tag to ProphetModels.pl call too

r4815 | henrylam | 2010-01-11 19:39:43 -0800 (Mon, 11 Jan 2010) | 1 line

[SpectraST] Allow user to define modifications in a file. Instructions will be in wiki shortly.

r4813 | henrylam | 2010-01-09 01:09:52 -0800 (Sat, 09 Jan 2010) | 1 line

[SpectraST] Minor inconsequential changes

r4811 | henrylam | 2010-01-06 00:07:22 -0800 (Wed, 06 Jan 2010) | 1 line

[SpectraST] Add a few modifications: oxidation/nitro/dimethylation/trimethylation

r4810 | henrylam | 2009-12-28 18:17:49 -0800 (Mon, 28 Dec 2009) | 1 line

[SpectraST] Simple fix to allow .sptxt files (after renaming to .msp) to be imported like .msp files

r4809 | henrylam | 2009-12-23 01:15:59 -0800 (Wed, 23 Dec 2009) | 1 line

[SpectraST] Filter by prob table (-cT option) allows any-charge matches if charge is not specified in prob table

r4808 | henrylam | 2009-12-23 00:49:18 -0800 (Wed, 23 Dec 2009) | 1 line

[SpectraST] Add \#include of C libraries to fix stand-alone compilation (which stops working in Ubuntu 9.10 (64-bit) for some reason.

r4807 | henrylam | 2009-12-22 17:50:34 -0800 (Tue, 22 Dec 2009) | 1 line

[SpectraST] Fix hidden bug in SpectraSTPeakList::operator=; make peakMap a class member (rather than passed around); implement findPeak (based on m/z)

r4805 | henrylam | 2009-12-22 17:18:19 -0800 (Tue, 22 Dec 2009) | 1 line

[SpectraST] Add -c_MGF option to print library in MGF format

r4804 | henrylam | 2009-12-22 17:12:11 -0800 (Tue, 22 Dec 2009) | 1 line

[SpectraST] Put DECOY or REV proteins at the back of the list in the Protein comment field

r4801 | henrylam | 2009-12-17 18:21:09 -0800 (Thu, 17 Dec 2009) | 1 line

[ProphetModels.pl] Check alternative_protein for non-decoys

r4800 | henrylam | 2009-12-17 18:19:17 -0800 (Thu, 17 Dec 2009) | 1 line

[calctppstat.pl] Initialize num_missed_cleavage; Allow 10+ charge; Check alternative_protein for non-decoys

r4798 | henrylam | 2009-12-15 00:50:21 -0800 (Tue, 15 Dec 2009) | 1 line

[RefreshParser] Fix seg fault when num_tol_term is not present, e.g. in OMSSA files

r4749 | henrylam | 2009-11-10 17:14:27 -0800 (Tue, 10 Nov 2009) | 1 line

[SpectraST] Fix bug of missing first peak when searching MGF files

r4729 | henrylam | 2009-10-28 19:09:47 -0700 (Wed, 28 Oct 2009) | 1 line

[SpectraST] Allow uppercase file extensions MGF, DTA, MSP for search mode

r4699 | henrylam | 2009-10-13 23:06:46 -0700 (Tue, 13 Oct 2009) | 1 line

[SpectraST] Fix bug where consensus spectra are not annotated -- introduced in r4610, Sept 8, 2009

r4674 | henrylam | 2009-10-04 23:14:53 -0700 (Sun, 04 Oct 2009) | 1 line

[SpectraST] Clean up fragmentation type handling

r4612 | henrylam | 2009-09-07 22:52:18 -0700 (Mon, 07 Sep 2009) | 1 line

[SpectraST] Improve book-keeping for mzXML file import.

r4611 | henrylam | 2009-09-07 21:10:24 -0700 (Mon, 07 Sep 2009) | 1 line

[SpectraST] PepXML import supports merged scans (when startScan and endScan are different, say ABCD.1234.1240.3): will fetch multiple scans from mzXML files and merge them by consensus algorithm before including in library.

r4610 | henrylam | 2009-09-07 21:05:58 -0700 (Mon, 07 Sep 2009) | 1 line

[SpectraST] Import unidentified spectra from mzXML files directly. Minor changes to SpectraSTReplicates's consensus code to facilitate clustering without identifications

r4609 | henrylam | 2009-09-07 00:49:46 -0700 (Mon, 07 Sep 2009) | 1 line

[SpectraST] For logging purpose, also count Remark=DECOY as decoys

r4537 | henrylam | 2009-08-06 21:43:15 -0700 (Thu, 06 Aug 2009) | 1 line

[SpectraST] Fix minor bug when Peptide objects are copied

r4527 | henrylam | 2009-08-04 20:21:53 -0700 (Tue, 04 Aug 2009) | 1 line

[XTandem] Fix wrong recommended params for NATIVE Tandem

r4526 | henrylam | 2009-08-04 19:21:26 -0700 (Tue, 04 Aug 2009) | 1 line

[SpectraST] Entry filter will treat value as double only when it's strictly all numbers

r4525 | henrylam | 2009-08-04 19:13:18 -0700 (Tue, 04 Aug 2009) | 1 line

[SpectraST] Enable plotspectrast to plot two library spectra head-to-tail

r4524 | henrylam | 2009-08-04 19:07:48 -0700 (Tue, 04 Aug 2009) | 1 line

[SpectraST] Non-peptide entries now use preceeding underscore as flag instead of angle brackets

r4523 | henrylam | 2009-08-04 19:01:58 -0700 (Tue, 04 Aug 2009) | 1 line

[SpectraST] New ubiquitin-like mods

r4522 | henrylam | 2009-08-04 18:59:28 -0700 (Tue, 04 Aug 2009) | 1 line

[SpectraST] Decoy peak reposition considers first annotation only

r4521 | henrylam | 2009-08-04 18:42:59 -0700 (Tue, 04 Aug 2009) | 1 line

[SpectraST] Lib2HTML includes column of precursor m/z

r4507 | henrylam | 2009-07-31 19:36:47 -0700 (Fri, 31 Jul 2009) | 1 line

[SpectraST] Fix minor bug with option qualityImmuneProbThreshold when used in spectrast_create.params

eng_jk

XPRESS

Added support for intensity ratios (versus area based ratios) and specifying negative mass offsets. XPRESS includes better support for highres data by optionally summing individual isotope peaks for chromatogram reconstruction.

Added minimum chromatrogram ion count parameter -c<num>. This parameter filters out entries from being quantified unless the reconstruction chromatogram meets the minimum number of peaks specified.

Added -l label free option. This option will calculate stats on precursor ions only. Resulting analysis is labeled as 'xpresslabelfree' in pep.xml.


MzXML2Search

Add -N option to print out top N most intense peaks in a spectrum. Needed for large peaklists from new instrument as Mascot will complain if input peak list exceeds 10,000 count.

zhisun

r4784 | zhisun | 2009-11-30 13:02:05 -0800 (Mon, 30 Nov 2009) | 1 line

Chris Paulse modified the script and made it more permissive regarding the precursorCharge target string (doesn’t expect space immediately after the close quote.)

r4545 | zhisun | 2009-08-07 15:02:14 -0700 (Fri, 07 Aug 2009) | 1 line

solve memory problem

csherwood

r4816 | csherwood | 2010-01-12 10:52:52 -0800 (Tue, 12 Jan 2010) | 1 line

[MaRiMba Merge] Adding/updating all MaRiMba-related files for the full integration of MaRiMba into the TPP.

spacepod

r4972 | spacepod | 2010-05-10 12:24:18 -0700 (Mon, 10 May 2010) | 2 lines

[build process] 1) add dectection for 64-bit OS X systems; 2) use macports vs fink search paths for extra libraries (can add detection, if requested)

r4971 | spacepod | 2010-05-10 12:21:03 -0700 (Mon, 10 May 2010) | 2 lines

[PepXMLViewer] adding casts to work under boost 1.43.0

r4967 | spacepod | 2010-05-04 17:20:10 -0700 (Tue, 04 May 2010) | 2 lines

[ASAPRatioPeptideParser] adding experimental wavelet smoothing. Test using new ASAPRatioPeptideParser -w option. From WaveletQuant implmentation, http://www.biomedcentral.com/1471-2105/11/219

r4922 | spacepod | 2010-03-31 16:21:57 -0700 (Wed, 31 Mar 2010) | 2 lines

[Makefile] removing extra tab character

r4921 | spacepod | 2010-03-31 11:53:14 -0700 (Wed, 31 Mar 2010) | 2 lines

[linux install] generalizing ubuntu 9.04 install to 9.10 as well (tested)

r4872 | spacepod | 2010-02-10 16:19:05 -0800 (Wed, 10 Feb 2010) | 1 line

[OS requirements] updating ubuntu 8.10 install

r4785 | spacepod | 2009-11-30 17:46:38 -0800 (Mon, 30 Nov 2009) | 1 line

[mingw build] updates for mingw build

r4660 | spacepod | 2009-09-28 14:17:22 -0700 (Mon, 28 Sep 2009) | 3 lines

[c to c++ cleanup] catching a few files that svn got confused on the first time.


r4659 | spacepod | 2009-09-28 14:07:53 -0700 (Mon, 28 Sep 2009) | 3 lines

[c to c++ cleanup] catching a few files that svn got confused on the first time.


r4658 | spacepod | 2009-09-28 14:02:07 -0700 (Mon, 28 Sep 2009) | 3 lines

[c to c++ cleanup] catching a few files that svn got confused on the first time.


r4657 | spacepod | 2009-09-28 13:44:33 -0700 (Mon, 28 Sep 2009) | 4 lines

[c to c++ rename] merging changes to convert file extensions and build process from c to c++, from cpprename. fully tested in 'cpprename' branch.


r4656 | spacepod | 2009-09-28 13:19:44 -0700 (Mon, 28 Sep 2009) | 1 line

[windows builds] updating paths for boost, expat dependencies; from cpprename branch

r4655 | spacepod | 2009-09-28 12:25:19 -0700 (Mon, 28 Sep 2009) | 1 line

[restoring trunk/tpp to cleaner history, before c->c++ thrashing

r4587 | spacepod | 2009-08-24 12:13:54 -0700 (Mon, 24 Aug 2009) | 1 line

[mingw build] adding script for building TPP under mingw, so that it's easier to get this going from outside the mingw/msys environment.

r4573 | spacepod | 2009-08-13 17:48:57 -0700 (Thu, 13 Aug 2009) | 1 line

[pwiz] attempting re-adding local copies in stages

r4572 | spacepod | 2009-08-13 17:47:42 -0700 (Thu, 13 Aug 2009) | 1 line

[pwiz] attempting re-adding local copies in stages

r4571 | spacepod | 2009-08-13 17:46:34 -0700 (Thu, 13 Aug 2009) | 1 line

[pwiz] attempting re-adding local copies in stages

r4570 | spacepod | 2009-08-13 17:45:39 -0700 (Thu, 13 Aug 2009) | 1 line

[pwiz] attempting re-adding local copies in stages

r4569 | spacepod | 2009-08-13 17:45:09 -0700 (Thu, 13 Aug 2009) | 1 line

[pwiz] attempting re-adding local copies in stages

r4568 | spacepod | 2009-08-13 17:43:43 -0700 (Thu, 13 Aug 2009) | 1 line

[pwiz] attempting re-adding local copies in stages

r4567 | spacepod | 2009-08-13 17:39:50 -0700 (Thu, 13 Aug 2009) | 2 lines

[pwiz] grr, trying again

r4566 | spacepod | 2009-08-13 16:56:51 -0700 (Thu, 13 Aug 2009) | 1 line

[pwiz] adding local copy, staging as sourceforge keeps rejecting large checkins

r4565 | spacepod | 2009-08-13 16:56:05 -0700 (Thu, 13 Aug 2009) | 1 line

[pwiz] adding local copy

r4564 | spacepod | 2009-08-13 15:59:03 -0700 (Thu, 13 Aug 2009) | 3 lines

[pwiz] zapping pwiz method using svn extern; will be replaced with sashimi's own copy


r4563 | spacepod | 2009-08-13 11:44:15 -0700 (Thu, 13 Aug 2009) | 2 lines

[pwiz] moving and updating pwiz notes to tpp/extern in prep for compressing pwiz

r4560 | spacepod | 2009-08-12 17:23:22 -0700 (Wed, 12 Aug 2009) | 3 lines

[moving win_lib into tpp/extern] moving files and making changes to reflect new locations. Followups likely.


r4557 | spacepod | 2009-08-12 14:23:21 -0700 (Wed, 12 Aug 2009) | 3 lines

[win_lib cleanup] part 1 of 2: merging changes from "win_lib-cleanup" branch to deal with compressed win_lib directories


slagelwa

r5044 | slagelwa | 2010-06-29 15:45:15 -0700 (Tue, 29 Jun 2010) | 2 lines

Numerous bug fixes, addtion of params directory

r4998 | slagelwa | 2010-05-28 14:49:00 -0700 (Fri, 28 May 2010) | 5 lines

Fixed issue with polling quitting too early Fixed issue with output files being written to the wrong place if the 

  input file was a link

Now handles mzXML.gz files

r4981 | slagelwa | 2010-05-18 15:18:07 -0700 (Tue, 18 May 2010) | 2 lines

Added qspectrast

r4980 | slagelwa | 2010-05-18 15:14:41 -0700 (Tue, 18 May 2010) | 2 lines

ignore propset again

r4979 | slagelwa | 2010-05-18 15:10:17 -0700 (Tue, 18 May 2010) | 2 lines

Setting some ignore properties

r4969 | slagelwa | 2010-05-07 10:02:16 -0700 (Fri, 07 May 2010) | 2 lines

Changed interface, lots of little fixes and changes

r4955 | slagelwa | 2010-04-20 16:20:36 -0700 (Tue, 20 Apr 2010) | 2 lines

Added README, quoted some paths, added back email functionality and fixed PBS not exporting users PATH

r4944 | slagelwa | 2010-04-14 17:35:00 -0700 (Wed, 14 Apr 2010) | 2 lines

Added inspect search engine and reworked the services architecture

r4943 | slagelwa | 2010-04-14 17:32:53 -0700 (Wed, 14 Apr 2010) | 3 lines

Now looks for both .mzXML and .mzML files (although all search engines might not be able to handel .mzML files...)

r4939 | slagelwa | 2010-04-12 15:41:45 -0700 (Mon, 12 Apr 2010) | 2 lines

Updated EC2 image, adding omssa support

r4933 | slagelwa | 2010-04-07 15:16:03 -0700 (Wed, 07 Apr 2010) | 2 lines

More errors in checkin

r4932 | slagelwa | 2010-04-07 14:33:03 -0700 (Wed, 07 Apr 2010) | 2 lines

Renaming extern directory to reflect more what the contents are, being high performance computing tools or "hpctools"

r4931 | slagelwa | 2010-04-07 14:29:10 -0700 (Wed, 07 Apr 2010) | 2 lines

Including some stuff left out of previous commit due to svn errors

r4930 | slagelwa | 2010-04-07 14:23:37 -0700 (Wed, 07 Apr 2010) | 2 lines

Added set of "qcmds" wrapper scripts which can be used to submit searches to a sun grid engine or PBS cluster. Restructured directory hierarchy so that new qcmds are in their own directory as is the aws stuff. Revamped the aws even more, many bug fixes.

r4916 | slagelwa | 2010-03-25 14:36:19 -0700 (Thu, 25 Mar 2010) | 2 lines

Cleaned up reporting, code in prepartion for supporing more search programs and more clusters

r4910 | slagelwa | 2010-03-19 16:28:55 -0700 (Fri, 19 Mar 2010) | 2 lines

Cleaned up parameters and documentation to prepare for a name change and addition of more search programs

r4909 | slagelwa | 2010-03-19 13:44:15 -0700 (Fri, 19 Mar 2010) | 5 lines

Changed file key format to postfix the filepath with the checksum instead of prefixing it. This way tools such as s3fm which treat keys containing a "/" as a file hierarchy can display and navigate better.

(Checksum in key is still a problem as the '/' character frequently occurs. Like to remove the checksum and rely on AWS checksum only).

r4908 | slagelwa | 2010-03-18 12:17:09 -0700 (Thu, 18 Mar 2010) | 13 lines

  • Spel institute correctly :)
  • No longer shuts down the client downloader after being idle for 30 minutes (searches can take longer than that...)
  • For each search request it now starts up a new EC2 instance, up to <MAX> instances instead of starting them all at once. Since the boot time is slightly

longer then the upload time this means that the new instance should be available shortly after the request gets submitted. This should solve the timeout problem with EC2 instances not getting work in time, and be a little less expensive as you are not starting all instances at once but as needed.

  • Added coded to report message errors and keep going. i noticed at least one situation were you could create a message error and the program would stop. this might address the "lost" message issue I saw as I suspect one of the nodes might have exited upon getting an message error.
  • Log files are now kept on each ec2 instance, and are copied back to the client when each are shutdown. should make it easier for any future debugging or reporting

~

r4907 | slagelwa | 2010-03-18 10:10:15 -0700 (Thu, 18 Mar 2010) | 2 lines

Included for testing/development

r4906 | slagelwa | 2010-03-18 10:09:39 -0700 (Thu, 18 Mar 2010) | 5 lines

Added a make target that uses the program aws to upload this program's distribution to a public S3 bucket. Each EC2 instance has a bootstartup script which will download this file and install it -- providing a nice automatic upgrade capability to the cloud.

r4905 | slagelwa | 2010-03-18 10:07:23 -0700 (Thu, 18 Mar 2010) | 4 lines

Updated/corrected end block to leave test files in tmp directory if(when) the tests fail. Fixed filename error bug in test itself that only became apparent after the code it was testing was changed.

r4897 | slagelwa | 2010-03-09 16:41:19 -0800 (Tue, 09 Mar 2010) | 3 lines

Updated documentation. Added a automatic "shutdown" feature of the search daemon to shutdown the EC2 node if no search requests have been received in over 15 minutes.

r4896 | slagelwa | 2010-03-09 15:44:17 -0800 (Tue, 09 Mar 2010) | 3 lines

Added threads parameter hack to fix timestamp issue in EC2 api

r4895 | slagelwa | 2010-03-09 15:18:18 -0800 (Tue, 09 Mar 2010) | 2 lines

Added target to upload new versions of the distro to S3 to be automatically deployed on the EC2 instances

r4876 | slagelwa | 2010-02-18 14:08:56 -0800 (Thu, 18 Feb 2010) | 2 lines

Skip xml elements that don't have attributes

r4711 | slagelwa | 2009-10-19 13:18:08 -0700 (Mon, 19 Oct 2009) | 2 lines

Use XML parser to parse params file. Strip leading/trailing blanks from taxon name

r4710 | slagelwa | 2009-10-19 13:13:34 -0700 (Mon, 19 Oct 2009) | 2 lines

Adding grep of threads parameter

r4667 | slagelwa | 2009-09-29 12:23:08 -0700 (Tue, 29 Sep 2009) | 4 lines

  • Fixed various related path bugs
  • Reorganized tandem objects
  • --start 0 works

r4624 | slagelwa | 2009-09-16 11:40:21 -0700 (Wed, 16 Sep 2009) | 2 lines

Set keyword properties

r4622 | slagelwa | 2009-09-15 16:11:02 -0700 (Tue, 15 Sep 2009) | 2 lines

One last file to move to fix import

r4621 | slagelwa | 2009-09-15 16:08:07 -0700 (Tue, 15 Sep 2009) | 2 lines

Fixing import as it when into the topdir instead of the subdir

r4620 | slagelwa | 2009-09-15 15:50:44 -0700 (Tue, 15 Sep 2009) | 1 line

Importing TPP AWS Search Tool

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