TPP:4.8.0 SVN Log

From SPCTools

(Difference between revisions)

Revision as of 02:48, 14 November 2014

r6516 | slagelwa | 2014-05-15 09:16:27 -0700 (Thu, 15 May 2014) | 2 lines

MERGE 4.7.1 branch development to trunk [r6505:HEAD]

r6517 | real_procopio | 2014-05-16 16:24:30 -0700 (Fri, 16 May 2014) | 1 line

[Petunia] Make dir listing *much* faster by removing calls to extremely inefficient tpplib_perl for file extension checking; restored PPM as default unit in AccMass option that somehow got clobbered during the merge back to trunk.

r6518 | real_procopio | 2014-05-16 18:45:24 -0700 (Fri, 16 May 2014) | 1 line

[Petunia] Added page for idconvert under Utilities; Broke out file browsing link (Files) to its own section for easy access

r6519 | real_procopio | 2014-05-22 20:14:35 -0700 (Thu, 22 May 2014) | 1 line

[TPP Models] Support for charting ASAPRatio pvalue data and model; display ASAP mean ratio in linear (as well as default log); added ability to highlight NSP bin and display peptide values alongside NSP table

r6520 | real_procopio | 2014-05-22 20:18:25 -0700 (Thu, 22 May 2014) | 1 line

[ProtXMLViewer] Added NSP bin link (goes to models page, with extra URL params); Added charge state to peptide link to PepXMLViewer (to get better set of related spectra)

r6521 | real_procopio | 2014-05-22 20:29:04 -0700 (Thu, 22 May 2014) | 1 line

[ASAPRatio pvalue] Write pvalue raw data and model into protXML (using a tmp file) so other tools can display/viz (the idea is to eventually get rid of the png file). Will require updates to schema! Also lowered bin size from 0.05 to 0.02 to get finer-grained model and values

r6522 | slagelwa | 2014-05-28 10:06:51 -0700 (Wed, 28 May 2014) | 3 lines

sort AMI list by most latest version first
include some example data (from course)

r6523 | real_procopio | 2014-05-28 12:35:53 -0700 (Wed, 28 May 2014) | 1 line

[TPP Models] Added support for FPKM model info and Libra parameters

r6524 | slagelwa | 2014-05-28 15:11:08 -0700 (Wed, 28 May 2014) | 6 lines

Changed element name "protein_summary" to "protein_summary_header" for the source_files and source_files_alt attributes in prot.xml files
Added comment and flow control so if correcting more than one attribute for a element if the 1st attribute was changed the 2nd or subsequent ones could be skipped.

r6525 | slagelwa | 2014-05-28 15:18:40 -0700 (Wed, 28 May 2014) | 2 lines

Instead of using the "," operator use the "|" operator

r6526 | slagelwa | 2014-05-29 08:38:24 -0700 (Thu, 29 May 2014) | 2 lines

Patch for recent versions of Ubuntu

r6527 | slagelwa | 2014-05-29 13:04:00 -0700 (Thu, 29 May 2014) | 2 lines

Set missing svn properties

r6528 | real_procopio | 2014-05-30 12:57:06 -0700 (Fri, 30 May 2014) | 8 lines

[ProtXMLViewer]

Implemented generic support for Libra (removed hard-coded channel masses and related code);
Added ability to sort by Libra channel
Added distinction between 'n/a' quant ratios vs 'no result' (all peptides rejected)
Added hard-coded secondary sort (by probability, or npeps)
Changed 'peptides' to 'PSMs' in column heading

r6529 | dshteyn | 2014-06-02 11:05:43 -0700 (Mon, 02 Jun 2014) | 1 line

PTMProphet: L[119] modification

r6530 | dshteyn | 2014-06-02 11:07:24 -0700 (Mon, 02 Jun 2014) | 1 line

plotspectrast.cgi: set GNUPLOT_BINARY definition at build time

r6531 | real_procopio | 2014-06-02 13:33:30 -0700 (Mon, 02 Jun 2014) | 1 line

[PepXMLViewer] Link PeptideProphet prob to new models page; run tpp_models if models page does not exist

r6532 | henryhlam | 2014-06-02 22:32:32 -0700 (Mon, 02 Jun 2014) | 1 line

[SpectraST] Fix bug when using similarity clustering. Singletons no longer have peaks zeroed out.

r6533 | dshteyn | 2014-06-03 11:23:33 -0700 (Tue, 03 Jun 2014) | 1 line

Respect: cleanup some code, default minprob 0.5

r6534 | henryhlam | 2014-06-03 21:03:52 -0700 (Tue, 03 Jun 2014) | 1 line

[SpectraST] Enable import from pepXML files with Percolator probabilities.

r6535 | henryhlam | 2014-06-03 21:39:59 -0700 (Tue, 03 Jun 2014) | 1 line

[SpectraST] New fragmentation type ETD-HR (specify with option -cIETD-HR at import): expects ETD fragments and assumes high resolution in peak annotation and alignment.

r6536 | henryhlam | 2014-06-06 05:34:36 -0700 (Fri, 06 Jun 2014) | 1 line

[SpectraST] Fix bug of not counting +1 spectra in unidentified libraries; also count +0 (unknown charge) spectra.

r6537 | henryhlam | 2014-06-06 05:45:46 -0700 (Fri, 06 Jun 2014) | 1 line

[SpectraST] Skip testing for +1 precursor if assigned precursor charge is >1, i.e. just trust the instrument.

r6538 | eng_jk | 2014-06-09 17:02:41 -0700 (Mon, 09 Jun 2014) | 2 lines

update Lorikeet viewer; now shows fragment mass error plot.

r6539 | real_procopio | 2014-06-09 19:23:43 -0700 (Mon, 09 Jun 2014) | 1 line

[PepXMLViewer] (bugfix) Fix detection of libra result in current spectrum node -- used for passing the Isobaric parameter to Lorikeet

r6540 | eng_jk | 2014-06-10 09:21:21 -0700 (Tue, 10 Jun 2014) | 2 lines

modify Lorikeet viewer to always show reporter ions checkbox

r6541 | eng_jk | 2014-06-10 09:54:41 -0700 (Tue, 10 Jun 2014) | 2 lines

remove "COMET" from the spectrum viewer title

r6542 | slagelwa | 2014-06-10 14:12:04 -0700 (Tue, 10 Jun 2014) | 29 lines

Updated Coment MS/MS search engine to 2014011

2014/06/03

Comet version "2014.01 rev. 1". This is a maintenance release of Comet. http://comet-ms.sourceforge.net

Release notes:

Re-use temporary arrays during spectral preprocessing for better memory management running under Windows, implemented by M. Hoopmann.
New parameter "override_charge" instructs Comet to override the listed precursor charge state in the input file with that specified by the "charge_range" parameter, implemented by D. Shteynberg.
Update MSToolkit to version r68 to support non-consecutive mzXML scans.
Bug fix: synchronize normal and sparse matrix xcorr scores when decoys are generated to fill in the xcorr distribution for the expectation score calculation, reported by D. Tabb.
Bug fix: buffer overflow issue on some linux distributions when retrieving host name, reported by K. Tamura.
Bug fix: close spawned threads, reported by M. Riffle.
Bug fix: corrected "sample_enzyme" reporting in pep.xml output, reported by L. Mendoza.
Bug fix: remove extra tab in txt output, reported by A. Kertesz-Farkas.
Bug fix: output file name gets mangled when .out files are used and the input is specified using a full path, reported by C. Hoogland.

r6543 | eng_jk | 2014-06-10 14:27:09 -0700 (Tue, 10 Jun 2014) | 2 lines

turn on mass error plot by default; clean up code

r6544 | slagelwa | 2014-06-11 11:08:44 -0700 (Wed, 11 Jun 2014) | 4 lines

Let's stop using a hardcoded path of "/ISB/" and instead use the mechanism that already existed for identifying the tpp installation "html" directory.

r6545 | dshteyn | 2014-06-13 13:59:00 -0700 (Fri, 13 Jun 2014) | 1 line

ProteinProphet: GROUPWTS used by default now and OCCAMS razor is now sharper than with GROUPWTS before this change. For old GROUPWTS behavior use SOFTOCCAM option. NOGROUPWTS added for original behavior without GROUPWTS used. Also added count of distinct peptide sequences.

r6546 | dshteyn | 2014-06-17 14:17:30 -0700 (Tue, 17 Jun 2014) | 1 line

Use stat to check for file's existence instead of try catch block that was crashing on windows.

r6547 | slagelwa | 2014-06-20 12:26:30 -0700 (Fri, 20 Jun 2014) | 5 lines

Merging in X!Tandem linux-13-05-16-1 over our copy of the source from gpm. I'm surprised this wasn't done when we did the upgrade to sledgehammer.

r6548 | slagelwa | 2014-06-23 14:08:57 -0700 (Mon, 23 Jun 2014) | 5 lines

Removed building of MPI version of X!Tandem pending some additional work in the Makefile. I'm not even sure these rules will work at this point and regardless we can't really support it and I don't believe its even used by most of our users.

r6549 | slagelwa | 2014-06-23 23:02:47 -0700 (Mon, 23 Jun 2014) | 6 lines

Now all object files and executable are in a architecture dependent location
Modernized it to use gcc's auodependency feature. Improves performance of build and fixes a number of flaws in the dependency rules.
Cleaned up the flags and linker commands
Added some documentation

r6550 | slagelwa | 2014-06-24 22:12:03 -0700 (Tue, 24 Jun 2014) | 3 lines

Corrected what looked like an issue with MacOS linker flags. Added -MP to gcc dependency creation, why not?

r6551 | dshteyn | 2014-06-26 13:17:50 -0700 (Thu, 26 Jun 2014) | 1 line

RespectParser: report each spectrum only once per file.

r6552 | slagelwa | 2014-06-26 16:38:25 -0700 (Thu, 26 Jun 2014) | 2 lines

Modifed so you can specify a download location

r6553 | slagelwa | 2014-06-27 10:07:09 -0700 (Fri, 27 Jun 2014) | 3 lines

Might as well make generating header file dependencies an option that is by default off

r6554 | real_procopio | 2014-06-30 16:41:58 -0700 (Mon, 30 Jun 2014) | 6 lines

[Petunia]

Added drop-down for quick file select; points to dbase/ and speclibs where appropriate;
Tool access menu items now span the entire row, with orange hover color;
Point to new ProtXMLViewer as default; leave link to legacy viewer;
Increased alpha opacity for menus.

r6555 | real_procopio | 2014-06-30 18:37:52 -0700 (Mon, 30 Jun 2014) | 1 line

[Petunia] Added basic interface for reSpect

r6556 | slagelwa | 2014-07-01 13:49:14 -0700 (Tue, 01 Jul 2014) | 2 lines

Removing deprecated and unused EC2 define condition

r6557 | real_procopio | 2014-07-03 17:46:01 -0700 (Thu, 03 Jul 2014) | 1 line

[PepXMLViewer] Replace hard-to-read ptm_peptide (which has in-line probs for each potential AA) with a graphical bar-chart of probs above the peptide sequence -- with mouse-over probs

r6558 | slagelwa | 2014-07-08 10:51:02 -0700 (Tue, 08 Jul 2014) | 2 lines

Removed execution property from C++ source code files

r6559 | slagelwa | 2014-07-08 13:22:49 -0700 (Tue, 08 Jul 2014) | 2 lines

Make HDF5 in the architect dependent build area

r6560 | slagelwa | 2014-07-10 08:52:39 -0700 (Thu, 10 Jul 2014) | 2 lines

No longer used.

r6561 | dshteyn | 2014-07-11 15:53:42 -0700 (Fri, 11 Jul 2014) | 1 line

InteractParser: remove errorneous path from spectrum name when occurring

r6562 | dshteyn | 2014-07-16 15:34:11 -0700 (Wed, 16 Jul 2014) | 1 line

InteractParser: BUGFIX When the MS datafile not read in successfully don't try to access the spectrumList or it crashes.

r6563 | dshteyn | 2014-07-17 10:58:44 -0700 (Thu, 17 Jul 2014) | 1 line

PTMProphet: BUGFIX better tracking of unspecified mods. fix reporting of masses combining a static and variable mod.

r6564 | dshteyn | 2014-07-17 13:38:57 -0700 (Thu, 17 Jul 2014) | 1 line

get_prots.pl: BUGFIX corrected pattern matching mistake, added JSON output. Include protein length in output.

r6565 | slagelwa | 2014-07-17 21:04:47 -0700 (Thu, 17 Jul 2014) | 5 lines

Simplified how version/build information is managed in TPP. Also now includes the "svnversion", if available, in the version info. And since the macro TPP_ARCH was only used by the program that generated the C++ source file I took that out too.

r6566 | slagelwa | 2014-07-17 21:09:29 -0700 (Thu, 17 Jul 2014) | 2 lines

Fixed a dependency and removed a debugging target

r6567 | real_procopio | 2014-07-18 14:54:41 -0700 (Fri, 18 Jul 2014) | 1 line

[TPP_models] Only run on files with .xml extensions

r6568 | real_procopio | 2014-07-18 15:06:36 -0700 (Fri, 18 Jul 2014) | 9 lines

[xinteract]

Run tpp_models.pl on all relevant files after the tmp directory shenanigans have taken place
Got rid of suppoprt for ancient (perl) ProteinProphet
Got rid of calls to extinct peptide and protein viewers
Cleaned up usage statement
Reformatted code to have consistent indentation
Other minor code cleanup

r6569 | real_procopio | 2014-07-18 16:09:42 -0700 (Fri, 18 Jul 2014) | 1 line

[PepXMLViewer] Remove link to more_pepanal.pl; replace with direct link to static html models page

r6570 | real_procopio | 2014-07-18 18:28:24 -0700 (Fri, 18 Jul 2014) | 1 line

[PepXMLViewer] Fix link to plotspectrast, broken by commir r6480

r6571 | henryhlam | 2014-07-22 01:31:24 -0700 (Tue, 22 Jul 2014) | 1 line

[SpectraST] Fix base_name field in pepXML file when outputDirectory option (-sO) is specified.

r6572 | real_procopio | 2014-07-22 14:57:52 -0700 (Tue, 22 Jul 2014) | 1 line

[SpectraST] Pass input file path when writing pepXML - updating 2 more calls

r6573 | real_procopio | 2014-07-22 18:28:16 -0700 (Tue, 22 Jul 2014) | 10 lines

[Petunia]

Allow search results to be written in directory other than where mz[X]ML files are:
- Comet and X!Tandem: use location of respective params file
- SpectraST: added input field for output dir (-sO option in SpaectraST)
Added 'dir_exists' validation
Highlight (red color) the words 'warning' and 'error' when viewing command output
Expanded Quick-File-Picker widget to list wildcards and directories
Link bare .dta files to Lorikeet viewer

r6574 | real_procopio | 2014-07-23 19:45:10 -0700 (Wed, 23 Jul 2014) | 8 lines

[ProtXMLViewer]

Added support for Gaggle and JSON output (for David's new graphical tool)
Added basic command-line support
Added 'single sequence entries' statistic
Added option to display all peptides in single page (like old viewer)
Warn user when no results passed filtering criteria
Minor formatting and css fixes

r6575 | henryhlam | 2014-07-25 02:27:55 -0700 (Fri, 25 Jul 2014) | 1 line

[SpectraST] Open modification search option.

r6576 | slagelwa | 2014-07-25 16:04:12 -0700 (Fri, 25 Jul 2014) | 13 lines

Updated list of EC2 types to include the latest generation of types.
- set the default type to now be m3.medium
Set the default password of the petunia user to 'guest'. Now can just hit "start instance" instead of getting the confusing error and then having to go set the password in the options.
Added a option for downloading and installing course data. Option is true by default.
Commented out empty "help" button on options dialog
Added small ico image
Replaced the ugly (in Luis opinion) welcome page with a simpler page containing links back to the proteomecenter site.

r6577 | slagelwa | 2014-07-28 11:48:04 -0700 (Mon, 28 Jul 2014) | 4 lines

Explicitly cast float to int to supress compiler warning that gets treated as an error.

r6578 | slagelwa | 2014-07-28 15:55:45 -0700 (Mon, 28 Jul 2014) | 4 lines

Make the welcome page links open in new window
Confirm page leaves
Reorder demo installation

r6579 | slagelwa | 2014-07-30 10:26:09 -0700 (Wed, 30 Jul 2014) | 3 lines

Tighten security on the rewrite rule/proxying so that we aren't running an open proxy relay

r6580 | slagelwa | 2014-08-04 14:30:28 -0700 (Mon, 04 Aug 2014) | 2 lines

Guess there is a new dll, cdt.dll, that's required.

r6581 | dshteyn | 2014-08-04 16:30:32 -0700 (Mon, 04 Aug 2014) | 1 line

SpectraST: Peptide new mod for DiMethyl-C13HD2

r6582 | henryhlam | 2014-08-07 23:55:40 -0700 (Thu, 07 Aug 2014) | 1 line

[SpectraST] Fix iRT regression bug.

r6583 | slagelwa | 2014-08-08 14:06:01 -0700 (Fri, 08 Aug 2014) | 2 lines

Changes to welcome page, fixed proxy url

r6584 | slagelwa | 2014-08-08 17:54:30 -0700 (Fri, 08 Aug 2014) | 2 lines

Create the bucket when EC2 instance launched

r6585 | eng_jk | 2014-08-13 11:01:52 -0700 (Wed, 13 Aug 2014) | 2 lines

add -s command line option to Libra to read reporter ion peaks from subsequent MS3 scans for Thermo data

r6586 | henryhlam | 2014-08-14 18:27:39 -0700 (Thu, 14 Aug 2014) | 1 line

Fix web path issues: Webpage generated by plot-msms should point to web directory rather than the local directory; also html was duplicated. Web path used by PepXMLViewer was hard-coded as /tpp/ in constants.h, should have been user-defined as TPP_WEB in Makefile.config.incl and set at make time. NOTE: Only LINUX install was fixed and tested.

r6587 | eng_jk | 2014-08-15 09:10:44 -0700 (Fri, 15 Aug 2014) | 2 lines

remove unused/unimplemented libra normalization channel

r6588 | eng_jk | 2014-08-18 17:43:26 -0700 (Mon, 18 Aug 2014) | 3 lines

disabled the <targetMS level=2" /> parameter; not relevant for iTRAQ/TMT use added <reporterFromMS3 value="0" /> parameter to control quantifying from subsequent MS3 scan; 0=no, 1=yes

r6589 | slagelwa | 2014-08-21 16:47:57 -0700 (Thu, 21 Aug 2014) | 4 lines

We work at the Institute for Systems Biology not at the Insitute for Systems Biology.

r6590 | slagelwa | 2014-08-22 13:21:52 -0700 (Fri, 22 Aug 2014) | 3 lines

ISB has moved.

r6591 | slagelwa | 2014-08-26 13:19:09 -0700 (Tue, 26 Aug 2014) | 2 lines

Removing old, defunct RemoteConvert checkin that was never used

r6592 | dshteyn | 2014-08-26 14:43:45 -0700 (Tue, 26 Aug 2014) | 1 line

Dimethyl mods

r6593 | dshteyn | 2014-08-26 14:48:58 -0700 (Tue, 26 Aug 2014) | 1 line

PTMProphet: correct issues reported by users dealing with n-terminal mods, e.g. Dimethyl

r6594 | dshteyn | 2014-08-26 14:54:08 -0700 (Tue, 26 Aug 2014) | 1 line

InterProphet: support for SWATHProphet

r6595 | dshteyn | 2014-09-03 11:29:37 -0700 (Wed, 03 Sep 2014) | 1 line

ProteoGrapher libraries

r6596 | dshteyn | 2014-09-03 11:33:19 -0700 (Wed, 03 Sep 2014) | 1 line

ProteoGrapher first commit

r6597 | dshteyn | 2014-09-03 11:43:19 -0700 (Wed, 03 Sep 2014) | 1 line

ProteoGrapher

r6598 | dshteyn | 2014-09-03 11:47:00 -0700 (Wed, 03 Sep 2014) | 1 line

ProteoGrapher

r6599 | dshteyn | 2014-09-03 12:26:23 -0700 (Wed, 03 Sep 2014) | 1 line

Fix typo in win installer

r6600 | dshteyn | 2014-09-03 13:05:04 -0700 (Wed, 03 Sep 2014) | 1 line

Update d3

r6601 | real_procopio | 2014-09-03 19:31:03 -0700 (Wed, 03 Sep 2014) | 1 line

[ProtXMLViewer] Capture protein length; Added link to David's new ProteoGrapher viz after json export; Change cursor to 'wait' when loading data

r6602 | real_procopio | 2014-09-04 14:25:48 -0700 (Thu, 04 Sep 2014) | 1 line

[Petunia]

Removed Cygwin paths support
Removed unused Libra channel option
Added new MS3 (Thermo) option to Libra
Moved updatePaths and idConvert pages under 'Files' section
Added link to ProteoGrapher for .prot.json files
Fixed typo in reSpect page

r6603 | slagelwa | 2014-09-05 10:31:27 -0700 (Fri, 05 Sep 2014) | 2 lines

Added test for incomplete files

r6604 | dshteyn | 2014-09-12 10:34:13 -0700 (Fri, 12 Sep 2014) | 1 line

PG.html: fix highlighting and error histogram.

r6605 | real_procopio | 2014-09-12 15:41:01 -0700 (Fri, 12 Sep 2014) | 1 line

[Libra] Remove long-deprecated code (and get rid of unused LIBRA_GET_FROM_STDIN define). Cleaned up code spacing/formatting as well.

r6606 | real_procopio | 2014-09-16 18:11:54 -0700 (Tue, 16 Sep 2014) | 1 line

[PepXMLViewer] Highlight modified AAs in ptm peptide string (html); bugfix correct web link to models page

r6608 | real_procopio | 2014-09-17 15:54:35 -0700 (Wed, 17 Sep 2014) | 1 line

[PepXMLViewer] Bug fix: find position of extension in the correct string! Fixes prob link to models page.

r6609 | dshteyn | 2014-09-18 10:37:33 -0700 (Thu, 18 Sep 2014) | 1 line

RespectParser: correct issue with multiple references to the same mzML file in one combination file such as created by iProphet.

r6611 | dshteyn | 2014-09-18 12:38:14 -0700 (Thu, 18 Sep 2014) | 1 line

RespectParser: Keep track on live threads and only join live threads.

r6613 | slagelwa | 2014-09-19 09:39:09 -0700 (Fri, 19 Sep 2014) | 2 lines

New comet release yesterday -- updating to 2014021.

r6615 | slagelwa | 2014-09-22 15:50:20 -0700 (Mon, 22 Sep 2014) | 2 lines

Fixed typo when outputting error

r6616 | henryhlam | 2014-09-22 19:15:25 -0700 (Mon, 22 Sep 2014) | 1 line

[SpectraST] New options for semi-empirical spectrum prediction for sequence-specific amino acid substitutions and PTMs

r6617 | slagelwa | 2014-09-23 08:43:25 -0700 (Tue, 23 Sep 2014) | 1 line

Fixing typo

r6618 | slagelwa | 2014-09-23 08:51:03 -0700 (Tue, 23 Sep 2014) | 1 line

Changes to the TPP version mechanism that were in my sandbox and had not been checked in. Uses a "BUILD_ID" comprised of the build date and svnrev.

r6623 | real_procopio | 2014-09-23 17:44:38 -0700 (Tue, 23 Sep 2014) | 1 line

[Petunia] Add option to run ProteinProphet from iProphet page

r6624 | henryhlam | 2014-09-24 03:47:23 -0700 (Wed, 24 Sep 2014) | 1 line

[SpectraST] Fix crash introduced by last check-in of semi-empirical spectrum generation feature.

r6626 | real_procopio | 2014-09-24 18:20:23 -0700 (Wed, 24 Sep 2014) | 1 line

[PepXMLViewer] Fix reference to analysis file for spectrum name link (displays N top hits from engine) in Comet; use comet hits viewer for Sequest links

r6630 | dshteyn | 2014-09-24 22:33:04 -0700 (Wed, 24 Sep 2014) | 1 line

PeptideProphetParser: If bad value in the model is found report and exit without generating giant log.

r6631 | dshteyn | 2014-09-24 22:34:59 -0700 (Wed, 24 Sep 2014) | 1 line

PepXMLViewer.cgi: bug fix in parsing and display of PTMProphet data.

r6634 | real_procopio | 2014-09-25 11:06:35 -0700 (Thu, 25 Sep 2014) | 1 line

[PepXMLViewer] Avoid memory leak bug by actually using arrays within their bounds. For ptm_peptide field

r6636 | slagelwa | 2014-09-25 11:32:08 -0700 (Thu, 25 Sep 2014) | 2 lines

Updating Comet to 2014022

r6637 | slagelwa | 2014-09-25 11:37:48 -0700 (Thu, 25 Sep 2014) | 2 lines

Make sure version is made

r6639 | slagelwa | 2014-09-25 13:38:36 -0700 (Thu, 25 Sep 2014) | 2 lines

Adding in release type

r6646 | dshteyn | 2014-09-26 16:00:07 -0700 (Fri, 26 Sep 2014) | 1 line

iProphet: printing all_ntt_probs twice for ntt=0 caused a bug that is now fixed.

r6649 | slagelwa | 2014-09-29 13:12:41 -0700 (Mon, 29 Sep 2014) | 3 lines

TPP-trunk: merging changes on branch that weren't initially checked into the trunk and then merged to branch.

r6651 | slagelwa | 2014-09-29 14:09:35 -0700 (Mon, 29 Sep 2014) | 2 lines

Checking in old sandbox modifications

r6689 | slagelwa | 2014-10-02 09:28:47 -0700 (Thu, 02 Oct 2014) | 3 lines

Fixing issue with home page showing "reSpect" as a tab instead of "Utilities".

r6691 | slagelwa | 2014-10-02 14:34:27 -0700 (Thu, 02 Oct 2014) | 3 lines

Updated version, download packages, and fixed and issue with the iframe sizing and clipping off the scrollbar on big pages.

r6695 | slagelwa | 2014-10-03 14:11:23 -0700 (Fri, 03 Oct 2014) | 2 lines

Minor change of documentation

r6709 | dshteyn | 2014-10-06 11:04:31 -0700 (Mon, 06 Oct 2014) | 1 line

tpp_gui.pl: use & to separate commands in windows, move towards stripping out run_in

r6710 | dshteyn | 2014-10-07 10:08:31 -0700 (Tue, 07 Oct 2014) | 1 line

RespectParser: installer

r6714 | dshteyn | 2014-10-08 10:19:10 -0700 (Wed, 08 Oct 2014) | 1 line

ASAPRatio: Enable wavelet option

r6717 | slagelwa | 2014-11-04 09:38:11 -0800 (Tue, 04 Nov 2014) | 4 lines

The installer now "fixes" an issue in XML::SAX on some Windows platforms that would result in the the warning "could not find ParserDetails.ini" being printed.

r6718 | slagelwa | 2014-11-04 17:27:52 -0800 (Tue, 04 Nov 2014) | 9 lines

Fixed issue with latest version of VM::EC2 throwing an exception now when describe_security_groups() called with a name parameter and the group doesn't exist. Now just get a list of all the groups and look to see if AMZTPP is a member.

Changed the group-description group-name to underscores -- guess they changed the API and did not make it backward compatible.

r6719 | slagelwa | 2014-11-04 17:37:42 -0800 (Tue, 04 Nov 2014) | 3 lines

Updating the required version for VM::EC2 to 1.28. Earlier versions don't appear to be forward compatible.

r6720 | slagelwa | 2014-11-05 14:44:15 -0800 (Wed, 05 Nov 2014) | 5 lines

Fixed issue with access key and secret key being passed as strings in the command line. On Windows the string gets passed to cmd.exe, which does nothing but pass on the 'quotes' resulting in bad credentials.

r6728 | dshteyn | 2014-11-06 10:13:03 -0800 (Thu, 06 Nov 2014) | 1 line

BUGFIX InterProphet: some runs failed when using multiple threads.

r6731 | real_procopio | 2014-11-07 13:07:25 -0800 (Fri, 07 Nov 2014) | 7 lines

[Petunia]

Added page for running DNA to AA 6-frame translation utility (translateDNA2AA-FASTA)
Test for amztpp prior to letting users enter their credentials
Catch "ParserDetails.ini" line from amztpp when expecting an XML-only response; add error message as mouse-over when amz log-in fails
Replaced deprecated 'endform' with supported 'end_form'

r6736 | real_procopio | 2014-11-11 16:36:07 -0800 (Tue, 11 Nov 2014) | 1 line

[ASAPRatio] Close file first, then delete it

r6740 | eng_jk | 2014-11-12 16:14:27 -0800 (Wed, 12 Nov 2014) | 2 lines

add MS1Intensity to the ms2 output format (for Scaffold)

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TPP:4.8.0 SVN Log

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Revision as of 02:48, 14 November 2014

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 [https://sourceforge.net/p/sashimi/code//6524 r6524] | slagelwa | 2014-05-28 15:11:08 -0700 (Wed, 28 May 2014) | 6 lines
-* Changed element name "protein_summary" to "protein_summary_header" for
+* Changed element name "protein_summary" to "protein_summary_header" for the source_files and source_files_alt attributes in prot.xml files
-  the source_files and source_files_alt attributes in prot.xml files
+* Added comment and flow control so if correcting more than one attribute for a element if the 1st attribute was changed the 2nd or subsequent ones could be skipped.
-* Added comment and flow control so if correcting more than one
-  attribute for a element if the 1st attribute was changed the 2nd or
-  subsequent ones could be skipped.
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 [ProtXMLViewer]
-- Implemented generic support for Libra (removed hard-coded channel masses and related code);
+* Implemented generic support for Libra (removed hard-coded channel masses and related code);
-- Added ability to sort by Libra channel
+* Added ability to sort by Libra channel
-- Added distinction between 'n/a' quant ratios vs 'no result' (all peptides rejected)
+* Added distinction between 'n/a' quant ratios vs 'no result' (all peptides rejected)
-- Added hard-coded secondary sort (by probability, or npeps)
+* Added hard-coded secondary sort (by probability, or npeps)
-- Changed 'peptides' to 'PSMs' in column heading
+* Changed 'peptides' to 'PSMs' in column heading
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 Release notes:
-- Re-use temporary arrays during spectral preprocessing for better memory
+* Re-use temporary arrays during spectral preprocessing for better memory  management running under Windows, implemented by M. Hoopmann.
-  management running under Windows, implemented by M. Hoopmann.
+* New parameter "override_charge" instructs Comet to override the listed  precursor charge state in the input file with that specified by the  "charge_range" parameter, implemented by D. Shteynberg.
-- New parameter "override_charge" instructs Comet to override the listed
+* Update MSToolkit to version r68 to support non-consecutive mzXML scans.
-  precursor charge state in the input file with that specified by the
+* Bug fix: synchronize normal and sparse matrix xcorr scores when decoys are  generated to fill in the xcorr distribution for the expectation score  calculation, reported by D. Tabb.
-  "charge_range" parameter, implemented by D. Shteynberg.
+* Bug fix: buffer overflow issue on some linux distributions when retrieving  host name, reported by K. Tamura.
-- Update MSToolkit to version r68 to support non-consecutive mzXML scans.
+* Bug fix: close spawned threads, reported by M. Riffle.
-- Bug fix: synchronize normal and sparse matrix xcorr scores when decoys are
+* Bug fix: corrected "sample_enzyme" reporting in pep.xml output, reported by L. Mendoza.
-  generated to fill in the xcorr distribution for the expectation score
+* Bug fix: remove extra tab in txt output, reported by A. Kertesz-Farkas.
-  calculation, reported by D. Tabb.
+* Bug fix: output file name gets mangled when .out files are used and the input is specified using a full path, reported by C. Hoogland.
-- Bug fix: buffer overflow issue on some linux distributions when retrieving
-  host name, reported by K. Tamura.
-- Bug fix: close spawned threads, reported by M. Riffle.
-- Bug fix: corrected "sample_enzyme" reporting in pep.xml output, reported
-  by L. Mendoza.
-- Bug fix: remove extra tab in txt output, reported by A. Kertesz-Farkas.
-- Bug fix: output file name gets mangled when .out files are used and the
-  input is specified using a full path, reported by C. Hoogland.
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 from gpm.  I'm surprised this wasn't done when we did the upgrade
 to sledgehammer.
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 * Now all object files and executable are in a architecture dependent location
-* Modernized it to use gcc's auodependency feature.  Improves performance of
+* Modernized it to use gcc's auodependency feature.  Improves performance of build and fixes a number of flaws in the dependency rules.
-  build and fixes a number of flaws in the dependency rules.
 * Cleaned up the flags and linker commands
 * Added some documentation
 Corrected what looked like an issue with MacOS linker flags.  Added -MP to gcc dependency creation, why not?
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 [xinteract]
-- Run tpp_models.pl on all relevant files after the tmp directory shenanigans have taken place
+* Run tpp_models.pl on all relevant files after the tmp directory shenanigans have taken place
-- Got rid of suppoprt for ancient (perl) ProteinProphet
+* Got rid of suppoprt for ancient (perl) ProteinProphet
-- Got rid of calls to extinct peptide and protein viewers
+* Got rid of calls to extinct peptide and protein viewers
-- Cleaned up usage statement
+* Cleaned up usage statement
-- Reformatted code to have consistent indentation
+* Reformatted code to have consistent indentation
-- Other minor code cleanup
+* Other minor code cleanup
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 [Petunia]
-- Allow search results to be written in directory other than where mz[X]ML files are:
+* Allow search results to be written in directory other than where mz[X]ML files are:
-  - Comet and X!Tandem: use location of respective params file
+** Comet and X!Tandem: use location of respective params file
-  - SpectraST: added input field for output dir (-sO option in SpaectraST)
+** SpectraST: added input field for output dir (-sO option in SpaectraST)
-- Added 'dir_exists' validation
+* Added 'dir_exists' validation
-- Highlight (red color) the words 'warning' and 'error' when viewing command output
+* Highlight (red color) the words 'warning' and 'error' when viewing command output
-- Expanded Quick-File-Picker widget to list wildcards and directories
+* Expanded Quick-File-Picker widget to list wildcards and directories
-- Link bare .dta files to Lorikeet viewer
+* Link bare .dta files to Lorikeet viewer
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 [ProtXMLViewer]
-- Added support for Gaggle and JSON output (for David's new graphical tool)
+* Added support for Gaggle and JSON output (for David's new graphical tool)
-- Added basic command-line support
+* Added basic command-line support
-- Added 'single sequence entries' statistic
+* Added 'single sequence entries' statistic
-- Added option to display all peptides in single page (like old viewer)
+* Added option to display all peptides in single page (like old viewer)
-- Warn user when no results passed filtering criteria
+* Warn user when no results passed filtering criteria
-- Minor formatting and css fixes
+* Minor formatting and css fixes
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 * Updated list of EC2 types to include the latest generation of types.
-   - set the default type to now be m3.medium
+** set the default type to now be m3.medium
-* Set the default password of the petunia user to 'guest'.  Now can
+* Set the default password of the petunia user to 'guest'.  Now can  just hit "start instance" instead of getting the confusing error and  then having to go set the password in the options.
-  just hit "start instance" instead of getting the confusing error and
+* Added a option for downloading and installing course data.  Option  is true by default.
-  then having to go set the password in the options.
-* Added a option for downloading and installing course data.  Option
-  is true by default.
 * Commented out empty "help" button on options dialog
 * Added small ico image
-* Replaced the ugly (in Luis opinion) welcome page with a simplier page
+* Replaced the ugly (in Luis opinion) welcome page with a simpler page  containing links back to the proteomecenter site.
-  containing links back to the proteomecenter site.
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 [https://sourceforge.net/p/sashimi/code//6577 r6577] | slagelwa | 2014-07-28 11:48:04 -0700 (Mon, 28 Jul 2014) | 4 lines
-Explicitly cast float to int to supress compiler warning that
+Explicitly cast float to int to supress compiler warning that gets treated as an error.
-gets treated as an error.
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 [https://sourceforge.net/p/sashimi/code//6589 r6589] | slagelwa | 2014-08-21 16:47:57 -0700 (Thu, 21 Aug 2014) | 4 lines
-We work at the Institute for Systems Biology not at the
+We work at the Institute for Systems Biology not at the Insitute for Systems Biology.
-Insitute for Systems Biology.
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 ISB has moved.
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 [https://sourceforge.net/p/sashimi/code//6602 r6602] | real_procopio | 2014-09-04 14:25:48 -0700 (Thu, 04 Sep 2014) | 1 line
-[Petunia] Removed Cygwin paths support; Removed unused Libra channel option; Added new MS3 (Thermo) option to Libra; Moved updatePaths and idConvert pages under 'Files' section; Added link to ProteoGrapher for .prot.json files; Fixed typo in reSpect page
+[Petunia]
+* Removed Cygwin paths support
+* Removed unused Libra channel option
+* Added new MS3 (Thermo) option to Libra
+* Moved updatePaths and idConvert pages under 'Files' section
+* Added link to ProteoGrapher for .prot.json files
+* Fixed typo in reSpect page
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 [https://sourceforge.net/p/sashimi/code//6603 r6603] | slagelwa | 2014-09-05 10:31:27 -0700 (Fri, 05 Sep 2014) | 2 lines
 [https://sourceforge.net/p/sashimi/code//6718 r6718] | slagelwa | 2014-11-04 17:27:52 -0800 (Tue, 04 Nov 2014) | 9 lines
-* Fixed issue with latest version of VM::EC2 throwing an exception now when
+* Fixed issue with latest version of VM::EC2 throwing an exception now when  describe_security_groups() called with a name parameter and the group   doesn't exist.   Now just get a list of all the groups and look to see if  AMZTPP is a member.
-  describe_security_groups() called with a name parameter and the group
-  doesn't exist.   Now just get a list of all the groups and look to see if
-  AMZTPP is a member.
-* Changed the group-description group-name to underscores -- guess they
+* Changed the group-description group-name to underscores -- guess they   changed the API and did not make it backward compatible.
-  changed the API and did not make it backward compatible.
 [https://sourceforge.net/p/sashimi/code//6719 r6719] | slagelwa | 2014-11-04 17:37:42 -0800 (Tue, 04 Nov 2014) | 3 lines
-Updating the required version for VM::EC2 to 1.28.  Earlier versions don't
+Updating the required version for VM::EC2 to 1.28.  Earlier versions don't appear to be forward compatible.
-appear to be forward compatible.
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 [https://sourceforge.net/p/sashimi/code//6720 r6720] | slagelwa | 2014-11-05 14:44:15 -0800 (Wed, 05 Nov 2014) | 5 lines
-Fixed issue with access key and secret key being passed as strings in
+Fixed issue with access key and secret key being passed as strings in the command line.  On Windows the string gets passed to cmd.exe, which does nothing but pass on the 'quotes' resulting in bad credentials.
-the command line.  On Windows the string gets passed to cmd.exe, which
-does nothing but pass on the 'quotes' resulting in bad credentials.
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 [Petunia]
-- Added page for running DNA to AA 6-frame translation utility (translateDNA2AA-FASTA)
+* Added page for running DNA to AA 6-frame translation utility (translateDNA2AA-FASTA)
-- Test for amztpp prior to letting users enter their credentials
+* Test for amztpp prior to letting users enter their credentials
-- Catch "ParserDetails.ini" line from amztpp when expecting an XML-only response; add error message as mouse-over when amz log-in fails
+* Catch "ParserDetails.ini" line from amztpp when expecting an XML-only response; add error message as mouse-over when amz log-in fails
-- Replaced deprecated 'endform' with supported 'end_form'
+* Replaced deprecated 'endform' with supported 'end_form'
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