From SPCTools

Changes since 4.5.2 release

------------------------------------------------------------------------ r5416 | pcbrefugee | 2011-05-31 13:00:39 -0700 (Tue, 31 May 2011) | 1 line [Makefiles] preserve compatibility with older minGW setups by testing for -static-libstdc++ support ------------------------------------------------------------------------ r5418 | slagelwa | 2011-06-01 16:59:29 -0700 (Wed, 01 Jun 2011) | 2 lines Major refit, pending some IE fixes ------------------------------------------------------------------------ r5419 | slagelwa | 2011-06-01 22:19:31 -0700 (Wed, 01 Jun 2011) | 2 lines Improved some error handling, fixed IE bug, removed unnecessary console declarations, added important console.info() declaration for IE ------------------------------------------------------------------------ r5420 | slagelwa | 2011-06-07 10:13:46 -0700 (Tue, 07 Jun 2011) | 2 lines Fixes for IE, rename title ------------------------------------------------------------------------ r5421 | pcbrefugee | 2011-06-09 14:20:58 -0700 (Thu, 09 Jun 2011) | 1 line [SpectraST] casts for quiet compile - log(int) is ambiguous on some compilers ------------------------------------------------------------------------ r5422 | pcbrefugee | 2011-06-09 14:23:47 -0700 (Thu, 09 Jun 2011) | 1 line [RTCalculator] casts and unused variable removal for quiet compile ------------------------------------------------------------------------ r5423 | pcbrefugee | 2011-06-09 14:24:50 -0700 (Thu, 09 Jun 2011) | 1 line need to include <float.h> for _isnan decl ------------------------------------------------------------------------ r5424 | pcbrefugee | 2011-06-09 14:38:21 -0700 (Thu, 09 Jun 2011) | 1 line [Makefile] help MSVC deal with inline decls in some additional GSL files we weren't using before by making a special header file for MSVC use ------------------------------------------------------------------------ r5425 | pcbrefugee | 2011-06-09 14:42:18 -0700 (Thu, 09 Jun 2011) | 1 line [gsl] add a couple of files we weren't using before to the VC8 build ------------------------------------------------------------------------ r5426 | pcbrefugee | 2011-06-09 14:44:14 -0700 (Thu, 09 Jun 2011) | 1 line [mzParser] use typedefs instead of define to avoid redefinition warnings, use _int32 instead of long when defining 32 bit integer type so it works in 64 bit windows ------------------------------------------------------------------------ r5427 | pcbrefugee | 2011-06-09 15:18:32 -0700 (Thu, 09 Jun 2011) | 1 line update MSVC8 build for use of zlib-1.2.5 and mzParser - probably incomplete for VC9 ------------------------------------------------------------------------ r5428 | pcbrefugee | 2011-06-09 16:47:58 -0700 (Thu, 09 Jun 2011) | 1 line [gsl msvc build] make sure gsl config.h has include path precedence within gsl build, copy vc8 changes to vc9 file (untested) ------------------------------------------------------------------------ r5429 | pcbrefugee | 2011-06-09 17:57:22 -0700 (Thu, 09 Jun 2011) | 1 line [VC8 build] add saxtandemhandler.cxx, don't use mzParser vcproj after all ------------------------------------------------------------------------ r5431 | dshteyn | 2011-06-15 14:36:17 -0700 (Wed, 15 Jun 2011) | 1 line RefreshParser: I->L conversion on peptide and proteins to map to all indistinguishable peptides in the proteins. ------------------------------------------------------------------------ r5433 | real_procopio | 2011-06-16 15:57:28 -0700 (Thu, 16 Jun 2011) | 1 line [windows installer] Adding Sqt2XML ------------------------------------------------------------------------ r5446 | slagelwa | 2011-07-13 15:05:09 -0700 (Wed, 13 Jul 2011) | 2 lines Finally checking in the new EC2 AMI scripts ------------------------------------------------------------------------ r5448 | pcbrefugee | 2011-07-13 17:48:06 -0700 (Wed, 13 Jul 2011) | 1 line [pentunia] added a link on the PepC page to the PepC paper, which is now on PubMed ------------------------------------------------------------------------ r5451 | henryhlam | 2011-07-14 19:40:43 -0700 (Thu, 14 Jul 2011) | 1 line [SpectraST] MRM table prints theoretical (not observed), accurate (to 4 decimal places) mass for Q3 ------------------------------------------------------------------------ r5457 | henryhlam | 2011-07-21 18:00:30 -0700 (Thu, 21 Jul 2011) | 1 line [SpectraST] Use theoretical mass in MRM tables -- missing change in last check-in ------------------------------------------------------------------------ r5459 | henryhlam | 2011-07-21 18:13:32 -0700 (Thu, 21 Jul 2011) | 1 line [SpectraST] Treat sptxt as msp for import (after ensuring no file overwrite); minor fixes ------------------------------------------------------------------------ r5468 | henryhlam | 2011-08-01 23:34:01 -0700 (Mon, 01 Aug 2011) | 1 line [SpectraST] Reduce chance of decoy hitting existing sequences leading to infinite-looping ------------------------------------------------------------------------ r5469 | henryhlam | 2011-08-02 00:14:52 -0700 (Tue, 02 Aug 2011) | 1 line [SpectraST] rand() out-of-bound fix for Windows ------------------------------------------------------------------------ r5471 | henryhlam | 2011-08-02 00:28:42 -0700 (Tue, 02 Aug 2011) | 1 line [SpectraST] Decoy: add two random AA plus K/R ------------------------------------------------------------------------ r5473 | slagelwa | 2011-08-02 11:18:35 -0700 (Tue, 02 Aug 2011) | 4 lines * Cleaned up duplicate params/ templates/ directories * Updated qtandem to handle .gz files ------------------------------------------------------------------------ r5474 | slagelwa | 2011-08-02 11:21:42 -0700 (Tue, 02 Aug 2011) | 2 lines * fixed params/ templates confusion ------------------------------------------------------------------------ r5480 | slagelwa | 2011-08-10 14:15:57 -0700 (Wed, 10 Aug 2011) | 11 lines Significant changes across the board that haven't been checked in. * Include EC2 name in working directory on instance to distinguish it * Fixed omssa path/files issues * Changed how polling of SQS message queues are tallied * Forking of upload/downloads * Fixed paths issue in pep.xml files * Cache directory changes ------------------------------------------------------------------------ r5481 | slagelwa | 2011-08-10 14:21:37 -0700 (Wed, 10 Aug 2011) | 2 lines fixing revision tag ------------------------------------------------------------------------ r5482 | slagelwa | 2011-08-10 14:28:37 -0700 (Wed, 10 Aug 2011) | 2 lines setting missing svn keywords property ------------------------------------------------------------------------ r5484 | eng_jk | 2011-08-11 11:36:24 -0700 (Thu, 11 Aug 2011) | 3 lines Add -e option to subsetdb for Andreas to allow for export of entries that do not match -N strings. Previously, the -N no-match strings only filtered out matches that passed the -M match strings. ------------------------------------------------------------------------ r5489 | slagelwa | 2011-08-17 12:17:09 -0700 (Wed, 17 Aug 2011) | 7 lines * Make sure relative filenames in databases are treated correctly. * Changed algorithm on when new instances are started. Now starts a new instance when the # running < # max and # pending > # running. Which might spawn extra instances due to eventual consistancy but shouldn't spawn more than can be processed. ------------------------------------------------------------------------ r5490 | dshteyn | 2011-08-17 15:55:23 -0700 (Wed, 17 Aug 2011) | 1 line PeptideProphetParser: update to correct problem with latest version of Myrimatch which removed some scores in the reports. ------------------------------------------------------------------------ r5491 | dshteyn | 2011-08-19 14:04:18 -0700 (Fri, 19 Aug 2011) | 1 line mzParser: Handling of highMZ lowMZ values for Agilent QTOF. ------------------------------------------------------------------------ r5495 | slagelwa | 2011-08-25 13:01:55 -0700 (Thu, 25 Aug 2011) | 26 lines * Changed name of amztppserver to the more standard amztppd * Changed to use the upstart init daemon on Ubuntu to start (and keep respawning) the amztpp daemon * Now checkst to make sure that when getting the # running instances that if the EC2 API returns something other than a list it doesn't crash * Changed/added error message if a file to be uploaded doesn't actually exist * Changed timeout on nodes to 10 minutes to equal the same timeout on the client (and reduce the opportunity of nodes running longer than needed) * Fixed/changed the algorithm for deciding to start more nodes. Now starts nodes if pending > running & pending > started * Message handles for services being executed are now written to the file system and removed after the service is completed. This is done to so that if the daemon unexpectly quits and is restarted the message isn't ignored for the timeout but instead is just removed. * uses checksum of file instead of checksum of gzipped file. (Didn't know that the same file contents in two different files results in different gzipped checksums.) * Shutdown only on exit now, always make sure srv message is deleted in case it is interrupted by an exit or signal, and always put the file to S3. * New "-s" option for tppamzd to control whether or not to shutdown on exit ------------------------------------------------------------------------ r5501 | henryhlam | 2011-09-01 05:43:09 -0700 (Thu, 01 Sep 2011) | 1 line [SpectraST] Fix rare error when S/N calculation failed due to too few peaks outside precursor region ------------------------------------------------------------------------ r5504 | dshteyn | 2011-09-20 12:53:23 -0700 (Tue, 20 Sep 2011) | 1 line PTMProphetParser: changes to the algorithm to make it work smoother and with better results. ------------------------------------------------------------------------ r5507 | slagelwa | 2011-09-23 14:09:08 -0700 (Fri, 23 Sep 2011) | 1 line Merged branch 4.5 (r5415:5505) into the trunk ------------------------------------------------------------------------ r5508 | dshteyn | 2011-09-23 14:36:13 -0700 (Fri, 23 Sep 2011) | 1 line SpectraSTLIB: adding randomization of spectrum function for PTMProphet. ------------------------------------------------------------------------ r5509 | dshteyn | 2011-09-23 15:04:39 -0700 (Fri, 23 Sep 2011) | 1 line PTMProphet: adding getVal functions for KDModel. ------------------------------------------------------------------------ r5510 | slagelwa | 2011-09-23 15:28:18 -0700 (Fri, 23 Sep 2011) | 5 lines Re-merged 4.5 changes in trunk. SVNTortise didn't list to my "accept branch" changes when I did the merge. (ALSO MEANS that the trunk changes in these two files will likely be lost) ------------------------------------------------------------------------ r5511 | dshteyn | 2011-09-23 16:20:07 -0700 (Fri, 23 Sep 2011) | 1 line Adding back support for Agilent QTOF mzML ------------------------------------------------------------------------ r5514 | dshteyn | 2011-09-23 17:04:33 -0700 (Fri, 23 Sep 2011) | 2 lines Fix typo ------------------------------------------------------------------------ r5515 | slagelwa | 2011-09-29 11:58:33 -0700 (Thu, 29 Sep 2011) | 6 lines * now removes the log files before submission * uses new conversion queues * no longer allows submissions with the --server flag and instead uses queues ------------------------------------------------------------------------ r5516 | ppatrick | 2011-10-04 08:57:14 -0700 (Tue, 04 Oct 2011) | 2 lines Changed from theoretical precursor mass to measured one to allow for narrower tolerances. ------------------------------------------------------------------------ r5517 | ppatrick | 2011-10-04 12:28:23 -0700 (Tue, 04 Oct 2011) | 2 lines Changed logic of xsl to speed up loading. ------------------------------------------------------------------------ r5518 | ppatrick | 2011-10-04 12:29:44 -0700 (Tue, 04 Oct 2011) | 2 lines increased min peptide probability to 0.8 from 0.5 ------------------------------------------------------------------------ r5519 | dshteyn | 2011-10-04 13:31:11 -0700 (Tue, 04 Oct 2011) | 1 line RefreshParser: make RefreshParser mapping of semi and non trypic peptides consistent with the search engine parameters unless overridden on the commandline (per Jimmy's and Vagisha's posts to spctools-dev of Jun 10 2011) ------------------------------------------------------------------------ r5520 | ppatrick | 2011-10-05 05:35:18 -0700 (Wed, 05 Oct 2011) | 2 lines Initialized preExt to account for incorrect file names being passed. ------------------------------------------------------------------------ r5521 | ppatrick | 2011-10-05 05:38:48 -0700 (Wed, 05 Oct 2011) | 2 lines Fixed buffer overruns in void XPressPeptideParser::parse(const char *xmlfile) and void XPressPeptideParser::validate_mzXMLfile() ------------------------------------------------------------------------ r5522 | ppatrick | 2011-10-05 05:40:47 -0700 (Wed, 05 Oct 2011) | 2 lines Fixed buffer overrun in void XPressPeptideParser::validate_mzXMLfile() ------------------------------------------------------------------------ r5523 | ppatrick | 2011-10-05 14:09:52 -0700 (Wed, 05 Oct 2011) | 3 lines Added Supplemental Activation Removed 0 intensity peaks ------------------------------------------------------------------------ r5524 | eng_jk | 2011-10-05 16:36:44 -0700 (Wed, 05 Oct 2011) | 2 lines quick mod to Patrick's buffer overrun fix (for non-sequential mzML scans) ------------------------------------------------------------------------ r5527 | eng_jk | 2011-10-06 14:16:52 -0700 (Thu, 06 Oct 2011) | 3 lines additional cleanup of yesterday's xpress buffer overrun fix; mainly changing size of a few allocated arrays which only affects mzML files with with non-sequential native IDs. ------------------------------------------------------------------------ r5528 | eng_jk | 2011-10-06 14:18:53 -0700 (Thu, 06 Oct 2011) | 2 lines change deflines to include which reading frame as part of accession ------------------------------------------------------------------------ r5529 | henryhlam | 2011-10-09 22:00:49 -0700 (Sun, 09 Oct 2011) | 1 line [util] Catch return values for smooth compiling ------------------------------------------------------------------------ r5530 | henryhlam | 2011-10-09 22:03:18 -0700 (Sun, 09 Oct 2011) | 1 line [mzParser] Pound-include stdint.h and catch return values for smooth compiling ------------------------------------------------------------------------ r5531 | henryhlam | 2011-10-09 23:57:02 -0700 (Sun, 09 Oct 2011) | 1 line [MzXML2Search] Option to remove charge-reduced precursors for ETD spectra (useful for search engines that do not have that feature) ------------------------------------------------------------------------ r5532 | henryhlam | 2011-10-09 23:59:27 -0700 (Sun, 09 Oct 2011) | 1 line [util] Catch return values for smooth compiling ------------------------------------------------------------------------ r5533 | henryhlam | 2011-10-10 00:02:43 -0700 (Mon, 10 Oct 2011) | 1 line [Tandem2XML] Fix wrong enzyme specificity for Lys-C ------------------------------------------------------------------------ r5534 | henryhlam | 2011-10-10 00:12:16 -0700 (Mon, 10 Oct 2011) | 1 line [xinteract] Move RefreshParser ahead of PeptideProphet to safeguard against some search engines' mangling the protein names and/or omitting NTT/NMC ------------------------------------------------------------------------ r5535 | henryhlam | 2011-10-10 00:19:18 -0700 (Mon, 10 Oct 2011) | 1 line [InteractParser] Fix OMSSA's problem with n-term mods ------------------------------------------------------------------------ r5536 | henryhlam | 2011-10-10 00:32:35 -0700 (Mon, 10 Oct 2011) | 1 line [InterProphet] More finely divided bins for error rate estimates. Important for modern, large datasets. ------------------------------------------------------------------------ r5537 | henryhlam | 2011-10-10 00:35:35 -0700 (Mon, 10 Oct 2011) | 1 line [PeptideProphet] More finely divided bins for error rate estimates. Important for modern, large datasets. ------------------------------------------------------------------------ r5538 | henryhlam | 2011-10-10 00:43:02 -0700 (Mon, 10 Oct 2011) | 1 line [Enzyme] Equate tryptic with trypsin ------------------------------------------------------------------------ r5548 | slagelwa | 2011-10-14 15:22:56 -0700 (Fri, 14 Oct 2011) | 4 lines * Set the default number of threads to 8 for tandem * Include a warning in the comments that values for three differential modifications are always needed ------------------------------------------------------------------------ r5552 | eng_jk | 2011-10-18 12:59:35 -0700 (Tue, 18 Oct 2011) | 2 lines replicate branch 5551 checkin to trunk for xpress/mzML fix ------------------------------------------------------------------------ r5553 | real_procopio | 2011-10-19 17:02:11 -0700 (Wed, 19 Oct 2011) | 1 line [dta2mzxml] Change 'plustwo' option to include lowest charge state found for a given scan; also make sure output is real mzXML ------------------------------------------------------------------------ r5555 | henryhlam | 2011-10-20 01:52:25 -0700 (Thu, 20 Oct 2011) | 1 line [SpectraST] Allow users to specify their own m/z range for MRM transitions (Q3) ------------------------------------------------------------------------ r5556 | henryhlam | 2011-10-20 01:59:58 -0700 (Thu, 20 Oct 2011) | 1 line [SpectraST] Consider all charges when library spectrum has charge 0 ------------------------------------------------------------------------ r5557 | henryhlam | 2011-10-20 02:01:34 -0700 (Thu, 20 Oct 2011) | 1 line [SpectraST] Allow import of non-peptide from MSP format ------------------------------------------------------------------------ r5558 | henryhlam | 2011-10-20 02:06:59 -0700 (Thu, 20 Oct 2011) | 1 line [SpectraST] New clustering algorithm. Saves memory, prevent deep recursion. ------------------------------------------------------------------------ r5560 | dshteyn | 2011-10-20 14:56:38 -0700 (Thu, 20 Oct 2011) | 1 line PTMProphetParser: NEW FEATURES amino acids and mass shifts are users settable as is mz tolerance, improved classification now outperforms ASCORE, EM is now default (new option NOEM). ------------------------------------------------------------------------ r5561 | real_procopio | 2011-10-20 17:24:09 -0700 (Thu, 20 Oct 2011) | 1 line [Petunia] Added version checking upon login; warn users if using an old version of TPP ------------------------------------------------------------------------ r5565 | mhoopmann | 2011-10-21 15:15:24 -0700 (Fri, 21 Oct 2011) | 1 line Fixed buffer overrun when reading small spectra compressed with zlib (compression increases spectrum size in these cases, hence the overrun). Moved stdint.h to linux build as it is not part of Visual Studio. ------------------------------------------------------------------------ r5567 | henryhlam | 2011-10-23 22:16:00 -0700 (Sun, 23 Oct 2011) | 1 line [SpectraST] High-mass accuracy MS2 support: frag type of CID-QTOF and HCD. Change to shuffleAllPeaks which is used by PTMProphet ------------------------------------------------------------------------ r5568 | dshteyn | 2011-10-24 10:56:36 -0700 (Mon, 24 Oct 2011) | 1 line PTMProphet: forgot to commit new function clearObs. ------------------------------------------------------------------------ r5571 | dshteyn | 2011-10-26 12:12:56 -0700 (Wed, 26 Oct 2011) | 1 line PepXMLViewer: Correct confusing probability column names in case of iProphet. ------------------------------------------------------------------------ r5572 | dshteyn | 2011-10-26 12:24:57 -0700 (Wed, 26 Oct 2011) | 1 line protxml2html.pl: The peptide links will now link out to PepXMLViewer instead of special separate parser. ------------------------------------------------------------------------ r5573 | eng_jk | 2011-10-26 16:27:35 -0700 (Wed, 26 Oct 2011) | 2 lines add option to dump ms1 scans as scan/mass/intensity; useful for generating plots ------------------------------------------------------------------------ r5575 | dshteyn | 2011-11-01 10:49:27 -0700 (Tue, 01 Nov 2011) | 1 line RTCatalog/RTCalc/RTModel : restructure code, check for fail condition (stddev==0), add gradient peptide feature, add worklist feature. ------------------------------------------------------------------------ r5576 | dshteyn | 2011-11-01 12:11:00 -0700 (Tue, 01 Nov 2011) | 1 line Additional typedefs, should probably be centralized. ------------------------------------------------------------------------ r5577 | dshteyn | 2011-11-01 12:17:09 -0700 (Tue, 01 Nov 2011) | 1 line RTModel: Additional update functions. ------------------------------------------------------------------------ r5578 | dshteyn | 2011-11-01 16:15:35 -0700 (Tue, 01 Nov 2011) | 1 line "iModelParser.cgi: Fix output of FDR plots when available under Windows." ------------------------------------------------------------------------ r5579 | dshteyn | 2011-11-01 16:17:12 -0700 (Tue, 01 Nov 2011) | 2 lines return a default url of http://localhost/ when WEBSERVER_URL is not set. ------------------------------------------------------------------------ r5581 | dshteyn | 2011-11-03 09:43:13 -0700 (Thu, 03 Nov 2011) | 1 line ProphetModel.pl bugfixes and updates. ------------------------------------------------------------------------ r5582 | dshteyn | 2011-11-03 12:40:58 -0700 (Thu, 03 Nov 2011) | 1 line Replace ~ with - to fix the whole XPress ~ character for negative mods hack problem. ------------------------------------------------------------------------ r5583 | dshteyn | 2011-11-03 12:54:22 -0700 (Thu, 03 Nov 2011) | 2 lines Fix extra paren typo ------------------------------------------------------------------------ r5584 | pcbrefugee | 2011-11-04 14:35:26 -0700 (Fri, 04 Nov 2011) | 1 line [msvc RAMP] use zlib 1.2.5 ------------------------------------------------------------------------ r5585 | pcbrefugee | 2011-11-04 14:37:14 -0700 (Fri, 04 Nov 2011) | 1 line tweaks for building gsl in msvc ------------------------------------------------------------------------ r5586 | dshteyn | 2011-11-04 14:56:44 -0700 (Fri, 04 Nov 2011) | 1 line XPressPeptideParser: BUGFIX handle negative mass difference ------------------------------------------------------------------------ r5587 | pcbrefugee | 2011-11-04 15:15:18 -0700 (Fri, 04 Nov 2011) | 1 line silence warnings about depecrated open(), lseek() etc ------------------------------------------------------------------------ r5588 | pcbrefugee | 2011-11-04 15:20:37 -0700 (Fri, 04 Nov 2011) | 1 line tweaks for quiet compile ------------------------------------------------------------------------ r5589 | pcbrefugee | 2011-11-04 15:32:45 -0700 (Fri, 04 Nov 2011) | 1 line [X!!Tandem] consider MPI version (OpenMPI vs others) when building X!!Tandem ------------------------------------------------------------------------ r5591 | dshteyn | 2011-11-04 15:46:58 -0700 (Fri, 04 Nov 2011) | 2 lines fix link to PepXMLViewer ------------------------------------------------------------------------ r5593 | pcbrefugee | 2011-11-04 16:37:00 -0700 (Fri, 04 Nov 2011) | 1 line undo my 5588 change, actual problem was with bad implementation of stroull in windows sysdepend.h ------------------------------------------------------------------------ r5596 | pcbrefugee | 2011-11-07 10:02:24 -0800 (Mon, 07 Nov 2011) | 1 line get current with ProteoWizard: their rev 3102 with considerable performance gains for mzML reading particularly across network shares ------------------------------------------------------------------------ r5597 | dshteyn | 2011-11-07 10:10:12 -0800 (Mon, 07 Nov 2011) | 1 line xinteract: fix bug passing parameters to XPress. ------------------------------------------------------------------------ r5598 | eng_jk | 2011-11-07 10:46:11 -0800 (Mon, 07 Nov 2011) | 3 lines Add minimum probability cutoff to quantify peptides (-q command line option; -p and -P already taken) Default cutoff is still at 0.5. Applies to both standard and labelfree modes ------------------------------------------------------------------------ r5599 | pcbrefugee | 2011-11-07 11:02:19 -0800 (Mon, 07 Nov 2011) | 1 line quiet a "not all control paths return a value" warning ------------------------------------------------------------------------ r5600 | pcbrefugee | 2011-11-07 11:06:34 -0800 (Mon, 07 Nov 2011) | 1 line [ProteoWizard] missed a few new additions to ProteoWizard codebase ------------------------------------------------------------------------ r5601 | pcbrefugee | 2011-11-07 12:08:50 -0800 (Mon, 07 Nov 2011) | 1 line [RAMP] tweaks for using ProteoWizard's RAMPAdapter interface ------------------------------------------------------------------------ r5602 | pcbrefugee | 2011-11-07 13:19:26 -0800 (Mon, 07 Nov 2011) | 1 line [xtandem] tweak for using updated pwiz to read mzML ------------------------------------------------------------------------ r5603 | dshteyn | 2011-11-07 15:38:36 -0800 (Mon, 07 Nov 2011) | 1 line PepXMLViewer.cgi: Added link to javascript MS/MS ions viewer. ------------------------------------------------------------------------ r5609 | dshteyn | 2011-11-08 13:34:55 -0800 (Tue, 08 Nov 2011) | 1 line PTMProphetParser: Clean up PTMProphet ------------------------------------------------------------------------ r5610 | dshteyn | 2011-11-08 13:41:03 -0800 (Tue, 08 Nov 2011) | 1 line Spectrast: Function to randomize spectra. ------------------------------------------------------------------------ r5611 | dshteyn | 2011-11-08 13:42:20 -0800 (Tue, 08 Nov 2011) | 1 line Spectrast: back out Makefile change. ------------------------------------------------------------------------ r5612 | dshteyn | 2011-11-08 14:39:05 -0800 (Tue, 08 Nov 2011) | 1 line MS-GFDB support ------------------------------------------------------------------------ r5613 | dshteyn | 2011-11-08 14:39:47 -0800 (Tue, 08 Nov 2011) | 1 line MS-GFDB support ------------------------------------------------------------------------ r5614 | dshteyn | 2011-11-08 14:40:38 -0800 (Tue, 08 Nov 2011) | 1 line MS-GFDB support ------------------------------------------------------------------------ r5615 | dshteyn | 2011-11-08 14:56:07 -0800 (Tue, 08 Nov 2011) | 1 line MS-GFDB support ------------------------------------------------------------------------ r5617 | dshteyn | 2011-11-08 15:29:04 -0800 (Tue, 08 Nov 2011) | 1 line MS-GFDB support ------------------------------------------------------------------------ r5618 | pcbrefugee | 2011-11-08 16:59:45 -0800 (Tue, 08 Nov 2011) | 1 line [XPressPeptideParser] remove unneeded "struct" in "struct InputStruct" that conflicted with actual declaration of InputStruct as a class. ------------------------------------------------------------------------ r5619 | pcbrefugee | 2011-11-09 16:19:16 -0800 (Wed, 09 Nov 2011) | 1 line [pwiz] these generated files were added to SVN by mistake, deleting ------------------------------------------------------------------------ r5620 | pcbrefugee | 2011-11-09 16:57:33 -0800 (Wed, 09 Nov 2011) | 1 line [win32 build] use xcopy instead of cp -Rf for better blocking until end of copy operation when setting up gsl win32 build ------------------------------------------------------------------------ r5621 | pcbrefugee | 2011-11-09 17:03:34 -0800 (Wed, 09 Nov 2011) | 1 line [xtandem + hadoop] a few tweaks to make it easier to mimic standard x!tandem behavior on a Hadoop node for performance comparison purposes ------------------------------------------------------------------------ r5622 | pcbrefugee | 2011-11-09 17:10:13 -0800 (Wed, 09 Nov 2011) | 1 line [pwiz] add a trigger to build that generated file I just pulled from SVN ------------------------------------------------------------------------ r5625 | pcbrefugee | 2011-11-10 12:26:31 -0800 (Thu, 10 Nov 2011) | 1 line workaround for compile issue with boost::thread + mingw + gcc4.5 ------------------------------------------------------------------------ r5626 | pcbrefugee | 2011-11-10 15:02:18 -0800 (Thu, 10 Nov 2011) | 1 line [pwiz] add #include <stdlib.h> to allow use of size_t in mingw gcc4.6.1 ------------------------------------------------------------------------ r5627 | pcbrefugee | 2011-11-10 15:48:39 -0800 (Thu, 10 Nov 2011) | 1 line handle a couple more openmpi install scenarios for X!!Tandem build ------------------------------------------------------------------------ r5628 | dshteyn | 2011-11-11 12:28:05 -0800 (Fri, 11 Nov 2011) | 1 line cometresult.cgi: Checking QUERY_STRING for ';' ------------------------------------------------------------------------ r5629 | dshteyn | 2011-11-11 12:29:42 -0800 (Fri, 11 Nov 2011) | 1 line protxml2html.pl and associated tools for viewing protXML: Removed passing of commands on QUERY_STRING ------------------------------------------------------------------------ r5630 | dshteyn | 2011-11-11 12:30:19 -0800 (Fri, 11 Nov 2011) | 1 line tpplib_perl.pm: centralize parsing of QUERY_STRING, and checking QS for ';' ------------------------------------------------------------------------ r5631 | dshteyn | 2011-11-11 12:54:57 -0800 (Fri, 11 Nov 2011) | 1 line protxml2html.pl and associated tools for viewing protXML: Removed passing of commands on QUERY_STRING ------------------------------------------------------------------------ r5633 | slagelwa | 2011-11-14 15:14:47 -0800 (Mon, 14 Nov 2011) | 2 lines Exit on error, we're at 4.5.0 now ------------------------------------------------------------------------ r5635 | slagelwa | 2011-11-14 16:08:04 -0800 (Mon, 14 Nov 2011) | 3 lines Fix pwiz for 4.5.0 ------------------------------------------------------------------------ r5636 | real_procopio | 2011-11-15 16:10:31 -0800 (Tue, 15 Nov 2011) | 1 line [NSP Viewer] Complete overhaul of this cgi: using Perl XML:Parser module, so no more system calls to xslt; potentially thousands of times faster than the old one, since we stop parsing once we reach the end of <protein_summary_header> . Prettier output, too. ------------------------------------------------------------------------ r5637 | pcbrefugee | 2011-11-16 09:38:00 -0800 (Wed, 16 Nov 2011) | 5 lines Build system tweaks and a couple of disambiguating mzParser file copy/renames to make it possible to choose between RAMP+pwiz and mzParser, and to build both libs at the same time. This with an eye toward putting mzML parser maintenance burden back on ProteoWizard now that its performance problems have been fixed. Involves changing "#include <Parsers/mzParser/mzParser.h>" to just "#include <mzParser.h>" in quite a number of files. Just add MSDATA_XML_READER=RAMP to your "make" command and TPP will build with RAMP+pwiz in ../build/$(ARCH)-RAMP. Performance meets or exceeds mzParser on local files and is considerably better than mzParser on network shares. The main point is that given the complexity and continued development of mzML, having multiple parsers in the community is a waste of time and effort. And it leaves the door open to TPP bypassing raw->XML conversion altogether. Also fixed the Makefile cut and paste messiness from the ever growing list of searchResult subtyoe header files with a centralized SEARCHRESULTS_H definition, similar to DISTRIBUTIONS_H, MIXTUREDISTRS_H etc. ------------------------------------------------------------------------ r5638 | pcbrefugee | 2011-11-16 12:40:59 -0800 (Wed, 16 Nov 2011) | 1 line back out some experimental cruft from previous commit ------------------------------------------------------------------------ r5639 | pcbrefugee | 2011-11-16 13:29:35 -0800 (Wed, 16 Nov 2011) | 1 line a bit more backing out of experimental cruft from previous commit ------------------------------------------------------------------------ r5640 | pcbrefugee | 2011-11-16 14:00:42 -0800 (Wed, 16 Nov 2011) | 1 line rename makefile variableS MSDATA_XML_READER_* to the more generally descriptive TPP_MSDATA_READER_* ------------------------------------------------------------------------ r5641 | pcbrefugee | 2011-11-16 14:57:16 -0800 (Wed, 16 Nov 2011) | 1 line have Spectrast place its objects files in $(OBJ_ARCH) like everybody else so we don't mingle mzParser and RAMP builds for SpectraST by accident ------------------------------------------------------------------------ r5646 | dshteyn | 2011-11-23 11:32:16 -0800 (Wed, 23 Nov 2011) | 1 line BUGFIX: Correct issue with iProphet probability filtering and naming of columns. ------------------------------------------------------------------------ r5649 | henryhlam | 2011-11-29 01:01:28 -0800 (Tue, 29 Nov 2011) | 1 line [SpectraST] Fix obscure bug with option passing; better error checking ------------------------------------------------------------------------ r5650 | henryhlam | 2011-11-29 01:28:20 -0800 (Tue, 29 Nov 2011) | 1 line [SpectraST] Fix repetitive immonium annotations; Revamp immonium annotation procedure to include more than one ion for some amino acids ------------------------------------------------------------------------ r5651 | slagelwa | 2011-11-29 12:06:28 -0800 (Tue, 29 Nov 2011) | 4 lines * Added another check for tandem program * Allow mzML files in qmascot and look for the various formats for results urls in the responses from Mascot ------------------------------------------------------------------------ r5652 | slagelwa | 2011-11-29 16:04:57 -0800 (Tue, 29 Nov 2011) | 4 lines Merging 4.5.1 branch changes into trunk (incl more than one change from released 4.5.1. Fingers crossed. ------------------------------------------------------------------------ r5655 | dshteyn | 2011-12-02 00:09:09 -0800 (Fri, 02 Dec 2011) | 1 line BUGFIX: correct count of iProphet results. ------------------------------------------------------------------------ r5656 | dshteyn | 2011-12-02 00:10:26 -0800 (Fri, 02 Dec 2011) | 1 line MS-GFDB support: Change linear transform to get more into the right range. ------------------------------------------------------------------------ r5661 | pcbrefugee | 2011-12-05 13:53:32 -0800 (Mon, 05 Dec 2011) | 1 line better name for Spectrast obj build directory (formerly could conflict with Spectrast execuatble itself) ------------------------------------------------------------------------ r5662 | pcbrefugee | 2011-12-05 13:55:32 -0800 (Mon, 05 Dec 2011) | 1 line restore changes that got nuked by last merge-from-branch ------------------------------------------------------------------------ r5663 | pcbrefugee | 2011-12-05 14:43:37 -0800 (Mon, 05 Dec 2011) | 1 line remove extra copy of SpectraSTPeakList::shiftAllPeaksRandomly introduced by latest merge from branch ------------------------------------------------------------------------ r5664 | pcbrefugee | 2011-12-05 15:02:56 -0800 (Mon, 05 Dec 2011) | 1 line remove extra line of code intrroduced by last merge from branch (this file now compiles, I do not assert that it's correct. I do not trust automated merges.) ------------------------------------------------------------------------ r5666 | real_procopio | 2011-12-06 17:19:52 -0800 (Tue, 06 Dec 2011) | 1 line [decoyFASTA] Gracefully deal with empty lines in input fasta file ------------------------------------------------------------------------ r5667 | real_procopio | 2011-12-06 17:20:58 -0800 (Tue, 06 Dec 2011) | 1 line [decoyFASTA] dos2unix... ------------------------------------------------------------------------ r5669 | pcbrefugee | 2011-12-08 10:20:24 -0800 (Thu, 08 Dec 2011) | 1 line {Makefile] fix a filename case sensitivity problem that VMWare masked on my system (!) ------------------------------------------------------------------------ r5670 | slagelwa | 2011-12-09 15:56:05 -0800 (Fri, 09 Dec 2011) | 2 lines Use special remote convert program ------------------------------------------------------------------------ r5671 | slagelwa | 2011-12-09 16:02:15 -0800 (Fri, 09 Dec 2011) | 2 lines Checking in correct version ------------------------------------------------------------------------ r5672 | slagelwa | 2011-12-12 14:48:38 -0800 (Mon, 12 Dec 2011) | 2 lines Checking it old fix for omssa and signal handling ------------------------------------------------------------------------ r5679 | real_procopio | 2011-12-16 17:09:52 -0800 (Fri, 16 Dec 2011) | 1 line [Petunia] Update trunk to current version of 4.5.x branch ------------------------------------------------------------------------ r5680 | slagelwa | 2011-12-19 16:02:30 -0800 (Mon, 19 Dec 2011) | 6 lines * Updated SQS queue names * Fixed tests * Supports EC2 regions now (requires latest Net::Amazon::EC2) * Still testing... ------------------------------------------------------------------------ r5681 | real_procopio | 2011-12-20 15:00:31 -0800 (Tue, 20 Dec 2011) | 1 line [Petunia] First attempt at allowing multiple commands per user; in preparation for Cloud/cluster integration. Still more work needed... ------------------------------------------------------------------------ r5682 | slagelwa | 2011-12-20 17:03:46 -0800 (Tue, 20 Dec 2011) | 2 lines Merged Luis changes using svn merge (which already were merged manually checked in) ------------------------------------------------------------------------ r5683 | slagelwa | 2011-12-20 18:03:20 -0800 (Tue, 20 Dec 2011) | 4 lines dding eol property to this file. Endlines have been changed between branch and trunk and here's hoping svn can resolve that. ------------------------------------------------------------------------ r5684 | slagelwa | 2011-12-20 18:11:06 -0800 (Tue, 20 Dec 2011) | 2 lines Merged Mike's branch fixes onto trunk ------------------------------------------------------------------------ r5685 | real_procopio | 2011-12-24 20:18:10 -0800 (Sat, 24 Dec 2011) | 1 line [Petunia] Spruced up jobs and command output page; deleting a session also deletes all of its command outputs, unless there is at least one in running status; commands output moved into user directory ------------------------------------------------------------------------ r5686 | dshteyn | 2011-12-27 16:01:53 -0800 (Tue, 27 Dec 2011) | 1 line InteractParser: handle more ways of representing compensationVoltage in mzXML. ------------------------------------------------------------------------ r5689 | slagelwa | 2012-01-03 10:33:54 -0800 (Tue, 03 Jan 2012) | 2 lines Completely revamped to work with Oracle (Sun) Grid Engine ------------------------------------------------------------------------ r5691 | slagelwa | 2012-01-06 14:01:53 -0800 (Fri, 06 Jan 2012) | 11 lines * Updated the log output to be a little clearer and include both the job start and finish time * Corrected output messages when trapping exit/signals/errors. Turns out you can't distinquish why SGE is killing your job (qdel vs limits). * For search engines that use mgf files for input if the file already exists it doesn't try to recreate it. (Running parallel search engines would cause problems with the file being overwritten while a search is in progress. Come to think of it I haven't completely closed this hole.) * Fixed path to remoteconvert problem for qconvert ------------------------------------------------------------------------ r5693 | spacepod | 2012-01-10 15:59:26 -0800 (Tue, 10 Jan 2012) | 1 line Setting native line-ending property on xtandem code. No functional change. ------------------------------------------------------------------------ r5699 | pcbrefugee | 2012-01-12 13:02:32 -0800 (Thu, 12 Jan 2012) | 1 line [build] add an optional "-noreplace" arg to regenerate_VersionInfo for use in MSVC debug builds where a current timestamp just doesn't matter, and only slows the edit-build-test cycle ------------------------------------------------------------------------ r5700 | pcbrefugee | 2012-01-12 13:03:58 -0800 (Thu, 12 Jan 2012) | 1 line casts for quiet compile ------------------------------------------------------------------------ r5701 | pcbrefugee | 2012-01-12 13:08:21 -0800 (Thu, 12 Jan 2012) | 1 line [build] adding MSVC10 project files. These work with VS2010 Pro, haven't tested with Express. ------------------------------------------------------------------------ r5702 | pcbrefugee | 2012-01-12 13:28:09 -0800 (Thu, 12 Jan 2012) | 1 line [build] adding MSVC10 project files. These work with VS2010 Pro, haven't tested with Express. ------------------------------------------------------------------------ r5703 | pcbrefugee | 2012-01-13 14:06:13 -0800 (Fri, 13 Jan 2012) | 1 line [pwiz] tweak for building with OSX 10.7 ------------------------------------------------------------------------ r5704 | pcbrefugee | 2012-01-13 14:07:46 -0800 (Fri, 13 Jan 2012) | 1 line [xtandem] tweak for building with MSVC10 ------------------------------------------------------------------------ r5705 | pcbrefugee | 2012-01-13 14:11:15 -0800 (Fri, 13 Jan 2012) | 2 lines [Tandem2XML] convert xtandem timestamp to a proper xsd:dateTime as required by pepXML schema. For example, "2011:07:14:16:51:35" converts to "2011-07-14T16:51:35". ------------------------------------------------------------------------ r5706 | pcbrefugee | 2012-01-16 16:07:55 -0800 (Mon, 16 Jan 2012) | 1 line tweaks to permit regression tests of pepXML originating with X!Tandem, which throws in a lot of timestamp and timing info, and calls everything a "parameter" instead of using a proper XML tag name. ------------------------------------------------------------------------ r5707 | spacepod | 2012-01-16 16:15:13 -0800 (Mon, 16 Jan 2012) | 1 line Calling out the errno.h include, as some *nix flavors don't do this automatically ------------------------------------------------------------------------ r5708 | dshteyn | 2012-01-17 13:09:36 -0800 (Tue, 17 Jan 2012) | 1 line D3 javascript library for compareProts.pl (for now). ------------------------------------------------------------------------ r5710 | henryhlam | 2012-01-18 00:37:28 -0800 (Wed, 18 Jan 2012) | 1 line [mzParser] Initialize collisionEnergy field to zero to avoid having uninitialized meaningless numbers showing up in library entries ------------------------------------------------------------------------ r5712 | spacepod | 2012-01-19 16:36:09 -0800 (Thu, 19 Jan 2012) | 1 line Deleting standalone makefile for readmzXML tool and moving build into main Makefile. Build was breaking on OS X 10.7 64-bit, and there was no apparent need for duplicating the complexity of the main Makefile again in the standalone one. Feel free to roll this back if it breaks anything. ------------------------------------------------------------------------ r5713 | spacepod | 2012-01-19 16:39:10 -0800 (Thu, 19 Jan 2012) | 1 line Deleting accidental commit of development target in Makefile. ------------------------------------------------------------------------ r5715 | dshteyn | 2012-01-23 11:44:33 -0800 (Mon, 23 Jan 2012) | 1 line PepXMLViewer, ASAPRatio: get PepXMLViewer to recognize wavelet smoothing in ASAPRatio. ------------------------------------------------------------------------ r5716 | dshteyn | 2012-01-23 11:45:09 -0800 (Mon, 23 Jan 2012) | 1 line PepXMLViewer, ASAPRatio: get PepXMLViewer to recognize wavelet smoothing in ASAPRatio. ------------------------------------------------------------------------ r5717 | dshteyn | 2012-01-23 11:47:24 -0800 (Mon, 23 Jan 2012) | 1 line Build: Get the build to work under CentOS with xtandem and PepC compiling. ------------------------------------------------------------------------ r5718 | dshteyn | 2012-01-23 11:49:37 -0800 (Mon, 23 Jan 2012) | 1 line Build: Get the build to work under CentOS with xtandem and PepC compiling. ------------------------------------------------------------------------ r5719 | dshteyn | 2012-01-23 11:51:07 -0800 (Mon, 23 Jan 2012) | 1 line mzxml2search: init variable for start and end scan ------------------------------------------------------------------------ r5720 | dshteyn | 2012-01-23 11:53:31 -0800 (Mon, 23 Jan 2012) | 1 line RAMP: mismatch new-delete fixed. ------------------------------------------------------------------------ r5721 | dshteyn | 2012-01-23 11:57:13 -0800 (Mon, 23 Jan 2012) | 1 line PepXMLViewer, ASAPRatio: get PepXMLViewer to recognize wavelet smoothing in ASAPRatio. ------------------------------------------------------------------------ r5722 | dshteyn | 2012-01-23 11:58:12 -0800 (Mon, 23 Jan 2012) | 1 line PepXMLViewer, ASAPRatio: get PepXMLViewer to recognize wavelet smoothing in ASAPRatio. ------------------------------------------------------------------------ r5723 | dshteyn | 2012-01-23 11:59:59 -0800 (Mon, 23 Jan 2012) | 1 line PepXMLViewer, ASAPRatio: get PepXMLViewer to recognize wavelet smoothing in ASAPRatio. ------------------------------------------------------------------------ r5724 | dshteyn | 2012-01-23 12:02:03 -0800 (Mon, 23 Jan 2012) | 1 line PTMProphet: default now updates the pepXML file with most likely modifications, option NOUPDATE retains original behavior. ------------------------------------------------------------------------ r5725 | dshteyn | 2012-01-23 12:06:56 -0800 (Mon, 23 Jan 2012) | 1 line perl_paths: modified for changine compareProts as it now needs to point to d3.js. ------------------------------------------------------------------------ r5726 | dshteyn | 2012-01-23 12:10:19 -0800 (Mon, 23 Jan 2012) | 1 line compareProts.pl: Now does a lot more, including outputting a D3 interactive plot for browsing proteins incommons between pairs or files. ------------------------------------------------------------------------ r5727 | slagelwa | 2012-01-23 12:35:36 -0800 (Mon, 23 Jan 2012) | 4 lines * qmascot: Fixed up mascot parameters a bit * qtandem: not all grid engines have a parallel engine called threads * qsequest: working again ------------------------------------------------------------------------ r5728 | slagelwa | 2012-01-23 12:37:24 -0800 (Mon, 23 Jan 2012) | 6 lines - added the pvm start/stop scripts for qsequest - no longer use "notify" option. This option sends a USR1 signal right before the job is stopped due to priority/load. Some of the subprocesses exit when they get this signal. ------------------------------------------------------------------------ r5729 | dshteyn | 2012-01-23 14:23:56 -0800 (Mon, 23 Jan 2012) | 1 line D3.js : Tweak d3 library to respond better to wousewheel zooms. ------------------------------------------------------------------------ r5730 | dshteyn | 2012-01-23 15:36:52 -0800 (Mon, 23 Jan 2012) | 1 line Remove building of SRMProphet (not yet public). ------------------------------------------------------------------------ r5731 | dshteyn | 2012-01-23 15:41:36 -0800 (Mon, 23 Jan 2012) | 1 line Fix bad function call ------------------------------------------------------------------------ r5733 | dshteyn | 2012-01-23 21:56:45 -0800 (Mon, 23 Jan 2012) | 1 line Fix broken build due to misplaced comments. ------------------------------------------------------------------------ r5734 | dshteyn | 2012-01-26 14:49:10 -0800 (Thu, 26 Jan 2012) | 1 line PTMProphet: NOUPDATE option implemented, default now updates the mods to most likely sites; auto-detect ETD or CID and set the appropriate ion types, bugfix on modification info for static mods with an additional variable mod on the same position (mass was wrongly computed before). ------------------------------------------------------------------------ r5735 | dshteyn | 2012-01-27 09:59:40 -0800 (Fri, 27 Jan 2012) | 1 line mzParser: BUGFIX activationMethod was not being populates. ------------------------------------------------------------------------ r5736 | slagelwa | 2012-02-01 12:47:15 -0800 (Wed, 01 Feb 2012) | 4 lines * Changed "threads" pvm to "serial" to align with name of pe on aegir * Fixed issue in qsequest with bash numerical comparision * Fixed issue in qsequest with input and output dir comparision ------------------------------------------------------------------------ r5739 | slagelwa | 2012-02-01 23:15:19 -0800 (Wed, 01 Feb 2012) | 6 lines Major revision. Modified file storage in S3 to match what's on filesystem and use the "standard" key naming mechansim by most 3rd party programs. This saves the hassle of dealing with updating paths everywhere and means that you can "browse" the repository using other tools. Links still present a problem, but they do anyhow for all 3rd party apps. ------------------------------------------------------------------------ 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 ------------------------------------------------------------------------