TPP:5.0.0 SVN Log
From SPCTools
Revision as of 00:02, 30 August 2016
r6654 | slagelwa | 2014-09-30 10:46:26 -0700 (Tue, 30 Sep 2014) | 3 lines
TPP5-Refactor: making branch from trunk to work on TPP5 changes to directory structure, source files, build system, etc..
r6655 | slagelwa | 2014-09-30 11:17:45 -0700 (Tue, 30 Sep 2014) | 4 lines
TPP5-Refactor: Rename all ".cxx" files as ".cpp". After a lengthy discussion we decided to standardize on the extension ".cpp" for all of the C++ source files in TPP.
r6656 | slagelwa | 2014-09-30 12:10:59 -0700 (Tue, 30 Sep 2014) | 2 lines
TPP5-Refactor: removing deprecated pwiz folder
r6657 | slagelwa | 2014-09-30 12:22:31 -0700 (Tue, 30 Sep 2014) | 4 lines
TPP5-Refactor: retired refresh_interact. This wasn't being compiled in the TPP build and when I tried to compile it just throws all kinds of errors.
r6658 | slagelwa | 2014-09-30 12:32:15 -0700 (Tue, 30 Sep 2014) | 3 lines
TPP5-Refactor: Renaming common to Common so that it conforms with the other directory names in src/.
r6659 | slagelwa | 2014-09-30 12:36:36 -0700 (Tue, 30 Sep 2014) | 3 lines
TPP5-Refactor: Renaming util to Util so that it conforms with the other directory names in src/.
r6660 | slagelwa | 2014-09-30 12:45:08 -0700 (Tue, 30 Sep 2014) | 2 lines
TPP5-Refactor: directories didn't get deleted when retired or renamed
r6661 | slagelwa | 2014-09-30 12:48:32 -0700 (Tue, 30 Sep 2014) | 3 lines
TPP5-Refactor: moved Enzyme/ to Common/Enzyme. Seems Enzyme would be something that's common to many TPP components.
r6662 | slagelwa | 2014-09-30 12:57:56 -0700 (Tue, 30 Sep 2014) | 3 lines
TPP5-Refactor: updating #include statements to reflect move of the Enzyme/ folder to Common/Enzyme/
r6663 | slagelwa | 2014-09-30 13:06:00 -0700 (Tue, 30 Sep 2014) | 3 lines
TPP5-Refactor: moved COVERAGE/ folder into src/Util and renamed it batchcoverage after the name of the program it truly is.
r6664 | slagelwa | 2014-09-30 13:23:23 -0700 (Tue, 30 Sep 2014) | 4 lines
TPP5-Refactor: Removing all Visual Studio project files. These are project files are or will be seriously out of date after all of the TPP-5 refactoring and we are not in a position to update or maintain them anymore.
r6665 | slagelwa | 2014-09-30 13:29:28 -0700 (Tue, 30 Sep 2014) | 3 lines
TPP5-Refactor: moving run_in, runperl, tpp_hostname, and setWin32Permissions to the Util/ directory because they are utilities.
r6666 | slagelwa | 2014-09-30 13:30:37 -0700 (Tue, 30 Sep 2014) | 2 lines
TPP5-Refactor: unused. (Visual Studio thing? for Brian Pratt?)
r6667 | slagelwa | 2014-09-30 13:32:20 -0700 (Tue, 30 Sep 2014) | 2 lines
TPP5-Refactor: unused Win32 batch file, remove deleted directory
r6668 | slagelwa | 2014-09-30 14:07:05 -0700 (Tue, 30 Sep 2014) | 2 lines
TPP5-Refactor: perl_paths goes away in the new system.
r6669 | slagelwa | 2014-09-30 14:37:18 -0700 (Tue, 30 Sep 2014) | 2 lines
TPP5-Refactor: rolling back the previous change
r6670 | slagelwa | 2014-09-30 14:39:14 -0700 (Tue, 30 Sep 2014) | 5 lines
TPP5-Refactor: moving xtandem out of extern/ and into src/Search as the new policy is to try to keep only truly extern things in extern and we've heavily modified X!Tandem.
r6671 | slagelwa | 2014-09-30 14:41:30 -0700 (Tue, 30 Sep 2014) | 2 lines
TPP5-Refactor: perl_paths goes away (again) in the new system.
r6672 | slagelwa | 2014-10-01 09:19:02 -0700 (Wed, 01 Oct 2014) | 2 lines
TPP5-Refactor: renaming cxx files as cpp
r6673 | slagelwa | 2014-10-01 09:39:13 -0700 (Wed, 01 Oct 2014) | 3 lines
TPP5-Refactor: moving hpctools out of extern/ as its not a 3rd party external requirement for TPP.
r6674 | slagelwa | 2014-10-01 09:43:26 -0700 (Wed, 01 Oct 2014) | 3 lines
TPP5-Refactor: removing Visual Studio project files for building zlib. We now just do everything under MingW.
r6675 | slagelwa | 2014-10-01 09:46:32 -0700 (Wed, 01 Oct 2014) | 3 lines
TPP5-Refactor: removing VisualStudio files from extern. No longer maintain them.
r6676 | slagelwa | 2014-10-01 09:51:16 -0700 (Wed, 01 Oct 2014) | 3 lines
TPP5-Refactor: switching from using comet executables to just compiling comet for the platform.
r6677 | slagelwa | 2014-10-01 09:51:54 -0700 (Wed, 01 Oct 2014) | 2 lines
TPP5-Refactor: removing bat files (not used anymore if ever).
r6678 | slagelwa | 2014-10-01 09:52:47 -0700 (Wed, 01 Oct 2014) | 2 lines
TPP5-Refactor: not sure what this was ever for.
r6679 | slagelwa | 2014-10-01 10:01:17 -0700 (Wed, 01 Oct 2014) | 3 lines
TPP5-Refactor: fix a minor issue with includes that more recent gcc compilers were tripping up on.
r6680 | slagelwa | 2014-10-01 10:07:41 -0700 (Wed, 01 Oct 2014) | 3 lines
TPP5-Refactor: MingW64 gcc compiler seems to already have defined _WIN32_WINNT and with warnings as errors this stops the compile.
r6681 | slagelwa | 2014-10-01 10:26:17 -0700 (Wed, 01 Oct 2014) | 3 lines
TPP5-Refactor: replacing unknown bzip2.dll file by using actual source and building what we need.
r6682 | slagelwa | 2014-10-01 10:28:14 -0700 (Wed, 01 Oct 2014) | 3 lines
TPP5-Refactor: adding two more patches to boost 1.54 for compiling under recent gcc compilers on Linux/MingW64
r6683 | slagelwa | 2014-10-01 10:32:37 -0700 (Wed, 01 Oct 2014) | 2 lines
TPP5-Refactor: removing executable property on archives
r6684 | slagelwa | 2014-10-01 10:33:18 -0700 (Wed, 01 Oct 2014) | 2 lines
TPP5-Refactor: replacing gzstream directory with archive and patch.
r6685 | slagelwa | 2014-10-01 10:39:09 -0700 (Wed, 01 Oct 2014) | 2 lines
TPP5-Refactor: upgrade libarchive archive and add gd and png
r6686 | slagelwa | 2014-10-01 10:40:15 -0700 (Wed, 01 Oct 2014) | 2 lines
TPP5-Refactor: remove unneeded zlib dll's
r6687 | slagelwa | 2014-10-01 12:07:16 -0700 (Wed, 01 Oct 2014) | 3 lines
TPP5-Refactor: update include definitions with new directory locations.
r6688 | slagelwa | 2014-10-01 13:50:47 -0700 (Wed, 01 Oct 2014) | 4 lines
TPP5-Refactor: the kwset search routines were under the removed refresh_interact but were used by refreshparser and spectrast. Extracted a copy into Common so they can be properly used in more than one place.
r6693 | slagelwa | 2014-10-03 11:00:31 -0700 (Fri, 03 Oct 2014) | 2 lines
TPP5-Refactor: removing unused deprecated programs/files from Util
r6694 | slagelwa | 2014-10-03 13:53:45 -0700 (Fri, 03 Oct 2014) | 2 lines
TPP5-Refactor: removing unused deprecated batch file
r6696 | slagelwa | 2014-10-03 14:15:50 -0700 (Fri, 03 Oct 2014) | 2 lines
TPP5-Version: bringing up to date with trunk
r6698 | slagelwa | 2014-10-03 14:22:00 -0700 (Fri, 03 Oct 2014) | 2 lines
TPP5-Refactor: Fixed ISB's name/address
r6699 | slagelwa | 2014-10-03 14:22:40 -0700 (Fri, 03 Oct 2014) | 2 lines
TPP5-Refactor: Removed as these don't appear to be used anywhere.
r6700 | slagelwa | 2014-10-03 14:23:50 -0700 (Fri, 03 Oct 2014) | 2 lines
TPP5-Refactor: doesn't appear to be used anywere
r6701 | slagelwa | 2014-10-03 14:24:40 -0700 (Fri, 03 Oct 2014) | 3 lines
TPP5-Refactor: use getLocalHTML() function instead of define macro for path location
r6702 | slagelwa | 2014-10-03 14:25:28 -0700 (Fri, 03 Oct 2014) | 2 lines
TPP5-Refactor: changes necessitated by recent GCC
r6703 | slagelwa | 2014-10-03 14:27:15 -0700 (Fri, 03 Oct 2014) | 3 lines
TPP5-Refactor: removing gd code as it shouldn't be used/necessary anymore with new GD in extern
r6704 | slagelwa | 2014-10-03 14:30:25 -0700 (Fri, 03 Oct 2014) | 22 lines
TPP5-Refactor: Updated include statements to reflect new directory structure and/or file naming policy -This line, and those below, will be ignored--
M mzXML/tools/mzXMLIndexer/indexmzXML.cpp M Quantitation/Libra/LibraPeptideParser/Quantitation.hpp M Quantitation/Libra/LibraPeptideParser/LibraPeptideParser.h M Visualization/InteractParser/InteractParser.h M Visualization/PepXMLViewer/PepXSAXHandler.cpp M Visualization/Pep3D/Pep3D_functions.cpp M Search/SpectraST/SpectraSTSearchOutput.hpp M Search/SpectraST/FileUtils.cpp M Search/SpectraST/plotspectrast.cpp M Search/SpectraST/SpectraSTPepXMLLibImporter.hpp M Search/SpectraST/SpectraSTMzXMLSearchTask.hpp M Search/SpectraST/SpectraSTMzXMLLibImporter.hpp M Search/SpectraST/SpectraSTTsvLibImporter.hpp M Validation/PTMProphetParser/PTMProphetParser.h M Visualization/PepXMLViewer/PepXField.cpp M Validation/Respect/RespectParser.h M Util/add_mz.cpp
r6705 | slagelwa | 2014-10-03 14:33:29 -0700 (Fri, 03 Oct 2014) | 2 lines
TPP5-Refactor: Adding stdin to appease GCC compiler
r6706 | slagelwa | 2014-10-03 14:39:48 -0700 (Fri, 03 Oct 2014) | 4 lines
TPP5-Refactor: Updated some of the target conditionals to use the more standard names. Also had to make some adjustments for functions/defintions that exist under MingW64's GCC but not MingW.
r6707 | slagelwa | 2014-10-03 14:43:40 -0700 (Fri, 03 Oct 2014) | 5 lines
TPP5-Refactor: Introducing new macro TPP_WIN32THREADS to conditionally compile in pthreads or winthreads. Can't simply rely on platform to determine this. Also a good idea to continue to follow this practice for similar functionality.
r6708 | slagelwa | 2014-10-03 16:26:06 -0700 (Fri, 03 Oct 2014) | 2 lines
TPP5-Refactor: removing more Visual Studio files
r6713 | slagelwa | 2014-10-08 09:42:00 -0700 (Wed, 08 Oct 2014) | 2 lines
TPP5-Refactor: Merging trunk r6654 through r6712 into 'TPP_files.nsh'
r6768 | slagelwa | 2014-12-09 15:22:14 -0800 (Tue, 09 Dec 2014) | 5 lines
- Updated ProteoWizards upgrade instructions, makefile more in alignment
with TPP5.0 built system
- Added SPAREParts (back?)
r6779 | slagelwa | 2014-12-23 16:01:39 -0800 (Tue, 23 Dec 2014) | 2 lines
Fixing error message
r6781 | slagelwa | 2014-12-31 14:23:45 -0800 (Wed, 31 Dec 2014) | 3 lines
Checking in my sandbox. Reorganized programs into a more Perl-ish structure.
r6783 | slagelwa | 2014-12-31 14:33:51 -0800 (Wed, 31 Dec 2014) | 3 lines
Missed these changes
r6784 | slagelwa | 2014-12-31 14:59:50 -0800 (Wed, 31 Dec 2014) | 2 lines
Moved contents of CGI to perl.
r6785 | slagelwa | 2014-12-31 15:06:38 -0800 (Wed, 31 Dec 2014) | 1 line
r6786 | slagelwa | 2014-12-31 15:17:02 -0800 (Wed, 31 Dec 2014) | 2 lines
Checking in my source
r6787 | slagelwa | 2014-12-31 15:20:54 -0800 (Wed, 31 Dec 2014) | 2 lines
Added a pwiz-win32 directory, updated README. Reworked Makefile
r6788 | slagelwa | 2014-12-31 15:27:35 -0800 (Wed, 31 Dec 2014) | 2 lines
These got moved
r6789 | slagelwa | 2014-12-31 15:28:34 -0800 (Wed, 31 Dec 2014) | 2 lines
Don't need an empty directory
r6793 | slagelwa | 2015-01-06 16:24:15 -0800 (Tue, 06 Jan 2015) | 41 lines
Numerous changes including:
- Switched over to using the Inno Installer
- Uses a include file build by install instead
of having to maintain a file containing the
files to install. (One mechanism for handling
installation).
- Installs Strawberry perl as an option
- "perl" checks reworked as it now can install
Strawberry perl
- "installation" check removed
- Reworked extern/ProteoWizard
- Major updates to Makefile
- Now includes a pwiz-win32 so we can have
better mgmt of windoze version
- Installs pwiz licenses
- Version of TPP is now found in the VERSION.mk
file. Which as its name implies is a Makefile that simply gets included by the other makefiles. This follows the standard VERSION file found in many open source projects. BTW, the build process makes a similar "BUILD.mk" file that contains the version *and* build information.
- XTandem makefile removed and new rules placed in
Search/Makefile
- Worked on URLs in Petunia...more to come
- Included back in Mayu
- Included back in a number of other missing
Linux programs
- Added first pass at a generic http-tpp.conf file
- Added/modified Makefiles in new make system
r6794 | slagelwa | 2015-01-07 00:48:17 -0800 (Wed, 07 Jan 2015) | 2 lines
TPP5-Refactor: merged trunk r6793 into branch
r6795 | slagelwa | 2015-01-07 09:24:43 -0800 (Wed, 07 Jan 2015) | 2 lines
Missed some merge changes.
r6796 | slagelwa | 2015-01-07 09:47:48 -0800 (Wed, 07 Jan 2015) | 4 lines
- Fixed another merge change.
- Renamed tppbin to tpp_bin to match what we call
everything else
r6797 | slagelwa | 2015-01-07 10:18:00 -0800 (Wed, 07 Jan 2015) | 5 lines
One last merge issue which exposed a interesting aspect about amztpp log files, their location. I decided maybe they shouldn't be placed in the top tpp dir and bin dir but instead in the users command dir.
r6799 | slagelwa | 2015-01-07 11:07:10 -0800 (Wed, 07 Jan 2015) | 2 lines
Users don't need no stink'n help in TPP5 ;)
r6800 | slagelwa | 2015-01-07 11:43:49 -0800 (Wed, 07 Jan 2015) | 5 lines
Moved the old prophet image from the help dir into images so it can be used in the model's parser that is going away. Rmemoved other references to the help dir.
r6801 | slagelwa | 2015-01-07 12:10:06 -0800 (Wed, 07 Jan 2015) | 2 lines
TPP5-Refactor: not used anymore
r6804 | slagelwa | 2015-01-11 21:58:23 -0800 (Sun, 11 Jan 2015) | 24 lines
Next big checkin from my sandbox:
- Attempted to make TPP installation relocatable and clean up the confusion
around constants/tpp_hooks/util.cpp. Now uses *one* mechanism for defining various configuration paths and urls instead of #defines call by functions that were wrapped in #defines. The configuration values can all be supplied at build time (say in a site.mk file).
- Added a "base url" configuration. We use to install the html and schema
folders in the web server's document root on windows. On linux, there didn't even appear to be a normal place for these. So I reconfigured the Apache directives to server cgi, html, and schema out of the TPP directory. And its now the same on Linux in Windows. I added a "data" dir which points to were user data is kept. And a url for using this.
- New httpd-tpp.conf file gets generated as part
of the build with the build configuration applied (cool)
- More updates to the various Makefiles
* Data, base url configured from make
- Added new "data_url" to support providing a data
prefix to urls (what /ISB/ always was)
- make debugging output *NOT* the default in pepxmlviewer
- I'm sure a bunch other changes I missed
r6805 | slagelwa | 2015-01-11 22:44:04 -0800 (Sun, 11 Jan 2015) | 11 lines
TPP5Refactor: Merged recent DDS changes on trunk into branch:
- PTMProphet: Auto-populate SpectraST Peptide modifications list to
allow for localizing novel mods.
- PepXMLViewer: BUGFIX regenerate index when a new column is added.
- PepXMLViewer.cgi: Correct issue with bad byte offsets in large files
found by Ulli(solved two problems long time to open the pepXML since index is bad, generated duplicate entries in the HTML view).
r6808 | slagelwa | 2015-01-13 21:36:23 -0800 (Tue, 13 Jan 2015) | 2 lines
TPP5-Refactor: Remaining parts from merge from trunk to branch
r6809 | slagelwa | 2015-01-13 21:38:42 -0800 (Tue, 13 Jan 2015) | 2 lines
TPP5-Refactor: Removed CGI dir as contents were moved to perl/
r6810 | slagelwa | 2015-01-13 23:05:45 -0800 (Tue, 13 Jan 2015) | 9 lines
TPP5-Refactor: merge in latest trunk changes
- r6806 | dshteyn | PepXMLViewer: once a column is added to the index,
keep it there always.
- r6807 | dshteyn | PTMProphet: auto-populate modifications not known to
SpectraST Peptide library.
r6812 | slagelwa | 2015-01-14 15:56:18 -0800 (Wed, 14 Jan 2015) | 3 lines
TPP5-Refactor: fixing a bug that Luis encounted when building it. (Or will).
r6813 | slagelwa | 2015-01-20 09:31:29 -0800 (Tue, 20 Jan 2015) | 2 lines
TPP5-Refactor: merged Luis's latest changes on trunk into branch
r6814 | slagelwa | 2015-01-21 16:21:19 -0800 (Wed, 21 Jan 2015) | 2 lines
TPP5-Refactor: would be nice if master makefile build the conf/ directory
r6821 | slagelwa | 2015-01-27 00:18:23 -0800 (Tue, 27 Jan 2015) | 5 lines
TP5-Refactor: merging latest trunk changes into branch
Merging r6813 through r6820 into 'perl' Merging r6810 through r6820 into 'src'
r6822 | slagelwa | 2015-01-27 00:22:48 -0800 (Tue, 27 Jan 2015) | 2 lines
Updated doc/fixed ISB alias
r6823 | slagelwa | 2015-01-27 00:36:43 -0800 (Tue, 27 Jan 2015) | 3 lines
TPP5-Refactor: correct change on TPP5 branch that accidently got backed out due to recent trunk merge.
r6824 | slagelwa | 2015-02-10 07:13:36 -0800 (Tue, 10 Feb 2015) | 1 line
TPP5-Refactor: merging trunk changes into branch
r6825 | slagelwa | 2015-02-11 08:46:20 -0800 (Wed, 11 Feb 2015) | 3 lines
- Now properly handles adding/removing directories from environment variables.
- Also cleaned up the code a little
r6826 | slagelwa | 2015-02-11 09:32:10 -0800 (Wed, 11 Feb 2015) | 3 lines
Renamed function call, problem was only seen on Windows.
r6827 | slagelwa | 2015-02-11 13:02:21 -0800 (Wed, 11 Feb 2015) | 2 lines
Cosmetic (or cosmic) fix
r6828 | slagelwa | 2015-02-11 13:04:26 -0800 (Wed, 11 Feb 2015) | 2 lines
Added UnxUtils back into the windows build
r6829 | slagelwa | 2015-02-11 14:22:21 -0800 (Wed, 11 Feb 2015) | 2 lines
Updated the instructions for Windows. Still incomplete but closer
r6840 | slagelwa | 2015-02-18 15:57:50 -0800 (Wed, 18 Feb 2015) | 2 lines
Added gsl to the linux build
r6841 | slagelwa | 2015-02-18 23:57:18 -0800 (Wed, 18 Feb 2015) | 4 lines
Added additional --without-lzma as DaveC discovered if you have lzma installed on your system then it compiles libarchive with support for lzma and then you have to include the -llzma flag.
r6842 | slagelwa | 2015-02-19 11:43:16 -0800 (Thu, 19 Feb 2015) | 11 lines
Added expat fann to the linux build so that it uses our version instead of the system version (if they even happen to be installed). Allows us to remove these from the build requirements. The only remaining ones are bzip2, libgd, and libpng. Are these commonly installed on systems? If not they either should be added or listed in the requirements.
Also made hdf5 get added if MZ5_SUPPORT is requested. Otherwise it gets ignored. I noticed on the Windows version is was getting built even though it isn't used. And that takes a LONG time....
r6843 | slagelwa | 2015-02-20 23:22:41 -0800 (Fri, 20 Feb 2015) | 2 lines
TPP-5: Adding our modified strawberry perl so we don't have to built it every time.
r6844 | slagelwa | 2015-02-20 23:25:49 -0800 (Fri, 20 Feb 2015) | 2 lines
Added FindBin::libs
r6845 | slagelwa | 2015-02-20 23:27:24 -0800 (Fri, 20 Feb 2015) | 3 lines
TPP5: now uses FindBin::libs to append to INC
also added a README for perl development
r6846 | slagelwa | 2015-02-21 00:05:37 -0800 (Sat, 21 Feb 2015) | 3 lines
TPP-5: Added perl Makefile.PL style tests with some very limited testing of
perl programs and modules
r6847 | slagelwa | 2015-02-22 23:37:45 -0800 (Sun, 22 Feb 2015) | 3 lines
TPP-5: want to leave the markers in the httpd.conf file for Windows as they need to be replaced by the Windows installer
r6848 | slagelwa | 2015-02-22 23:40:43 -0800 (Sun, 22 Feb 2015) | 5 lines
TPP-5 Updated strawberry perl again as it didn't really have FindBin::libs in it. Also threw in "-j" in the hopes I could convinence cpan to stop reading the settings from the users's home directory. Worked better but not completely so I added a error check to let the user know and move it out of the way.
r6849 | slagelwa | 2015-02-23 00:16:57 -0800 (Mon, 23 Feb 2015) | 2 lines
TPP-5: fix typo
r6850 | slagelwa | 2015-02-23 07:42:09 -0800 (Mon, 23 Feb 2015) | 2 lines
TPP-5: standardize on using mingw32 test
r6851 | slagelwa | 2015-02-23 22:45:32 -0800 (Mon, 23 Feb 2015) | 2 lines
TPP-5: use env to point to build area instead of source area
r6852 | slagelwa | 2015-02-24 21:30:51 -0800 (Tue, 24 Feb 2015) | 4 lines
TPP-5: Windows installer now fills in httpd.conf template as it was
being filled in on linux.
r6853 | slagelwa | 2015-03-03 01:08:40 -0800 (Tue, 03 Mar 2015) | 5 lines
TPP5: * Installer now honors data dir settings
* Installer properly fills out httpd conf file
* Cleaned up strawberry perl a little more
r6854 | slagelwa | 2015-03-04 07:27:00 -0800 (Wed, 04 Mar 2015) | 13 lines
TPP-5: In my endevour to make the build more configurable I added the ability to set the default URLs used in TPP from the command line. This sort of works to a point, but also exposes a shortcoming in MinGW/MSYS. It likes to mangle paths found in arguments to commands -- such as to GCC. Didn't know that.
So I documented this in the README, and had to come up with a lousy hack to get around it since there isn't a way to disable this function. The hack is to not start URL's provided on the command line with "/". Yeah, I know.
Also brought the make variable names more in aline with their corresponding
- defines.
r6861 | slagelwa | 2015-03-04 22:28:30 -0800 (Wed, 04 Mar 2015) | 4 lines
TPP5: * fixed some comet vs comet.exe funkiness on mingw32
* removed some paths from PERL5LIB on windows as strawberry perl adds
them already
r6865 | slagelwa | 2015-03-06 09:49:05 -0800 (Fri, 06 Mar 2015) | 3 lines
TPP5: Added some more documentation, fixed up http conf files after testing on Windows. Fixed tpp_gui's use of shebank line.
r6866 | slagelwa | 2015-03-07 13:35:59 -0800 (Sat, 07 Mar 2015) | 3 lines
TPP5: * added some more checking in the installer
* updated registery enviroment variables
r6873 | slagelwa | 2015-03-20 09:29:49 -0700 (Fri, 20 Mar 2015) | 14 lines
TPP-5: saving snapshot, many changes
* Changed TPP_DIR to SRC_DIR to be more similar to other names and
less confusing with the TPP_* environment variables
* Cleanup on licensing stuff. Still issue to fix
* Added few more perl modules
* Messaging in installer when updating env variables
* Fixed updating of tpp httpd configuration in installer
* Worked on TPP_* variable names
* More documentation
* Check build values for '/' vs '\'
* Many more...
r6875 | slagelwa | 2015-03-23 19:36:59 -0700 (Mon, 23 Mar 2015) | 8 lines
TPP5: * Updated Strawberry perl to 5.18.2.2
* Corrected issue with perl licenses not being there
* DEBUG=1 now builds with debugging flags
* make debug for building whole debugging tpp
* moved new get*() functions until util.h where they belong
* getWebserverRoot now returns tppdata value
r6877 | slagelwa | 2015-03-24 22:33:09 -0700 (Tue, 24 Mar 2015) | 13 lines
TPP5:
- removed runperl, doesn't seem to be used anywhere
- guess calctppstats really wants badly to live in cgi-bin
- fixed minor path issue in PepXMLViewer
- fixed a Win32 issue with system() (damn you #ifdef to hell in sysdepends.h
this needs to be cleaned up)
- yes, the path to TPP static web documents is in html/ not in /
I'd love to name this something other than html since it is so muc more than html files.. Common names found in other web frameworks include static/, public/, www/, htdocs/, resources/, assets/,
r6878 | slagelwa | 2015-03-24 22:44:39 -0700 (Tue, 24 Mar 2015) | 2 lines
TPP5: we don't use SWIG anymore
r6879 | slagelwa | 2015-03-25 00:13:13 -0700 (Wed, 25 Mar 2015) | 6 lines
TPP5: Probably really going to regret this but I removed the SWIG ifndefs
from sysdepend.h and reogranized/commented/cleaned up the legacy
sometimes backwards ifdef hell. Compiles under gcc on linux/ming32.
Can't say for MacOSX or Visual Studio.
r6880 | slagelwa | 2015-03-25 00:31:17 -0700 (Wed, 25 Mar 2015) | 3 lines
TPP5: removed run_in, not used anylonger. Also removed source file for
runperl as it got left around
r6881 | slagelwa | 2015-03-27 15:15:57 -0700 (Fri, 27 Mar 2015) | 3 lines
TPP5: added check for previous version of TPP to installer and warn that they
have to uninstall it first.
r6885 | slagelwa | 2015-03-31 22:32:10 -0700 (Tue, 31 Mar 2015) | 16 lines
TPP-5: Changed the way the install works on Windows. "make install" no longer builds a installer then runs it. Also removed the building of a "manifest" to give to the installer so it can the same make install that Linux does and just use the "recursefire" option in Inno to slurp in the installation directory. Makes Makefile much simpler and much easier to maintain. Only risk is that it pulls in unexpected files - so make sure you clean the install directory before making the installer.
The new targets to make this all happen are:
install - of course installer - packages up the installation directory into a installer setup - runs the installer (need a better name) uninstall - removes the installation directory
r6886 | slagelwa | 2015-03-31 22:42:45 -0700 (Tue, 31 Mar 2015) | 2 lines
TPP5: Install pwiz EULA licenses on Windows
r6887 | slagelwa | 2015-03-31 23:52:30 -0700 (Tue, 31 Mar 2015) | 3 lines
TPP5: Try to check for ActivePerl and ask users to uninstall it if they only installed it to run TPP
r6890 | slagelwa | 2015-04-01 09:33:22 -0700 (Wed, 01 Apr 2015) | 3 lines
TPP5: strawberry perl is now added back in as a optional component. Will have to come up with a mechanism to do the same with pwiz.
r6894 | slagelwa | 2015-04-01 21:49:29 -0700 (Wed, 01 Apr 2015) | 2 lines
TPP5: make uninstall ALWAYS run
r6897 | slagelwa | 2015-04-06 00:04:31 -0700 (Mon, 06 Apr 2015) | 9 lines
TPP5: Well we're back to the install writing a file to feed to the installer. I really wanted to go the "grab the installation directory" approach but it was too hard to separate out pwiz into a component. We probably could have lived without this being a component but I figured where there was one use case there was likely going to be another. On the plus side I made it a little simpler to read and understand. Oh and it means there is less change that we'll accidently pick something up in the build.
r6898 | slagelwa | 2015-04-06 00:05:12 -0700 (Mon, 06 Apr 2015) | 2 lines
TPP5: there is no 'pwd' on windows
r6899 | slagelwa | 2015-04-06 00:05:43 -0700 (Mon, 06 Apr 2015) | 2 lines
TPP5: static html files are in same location now
r6900 | slagelwa | 2015-04-06 00:06:40 -0700 (Mon, 06 Apr 2015) | 3 lines
TPP5: latest version of strawberry perl was yelling about use strict and bare endhtml calls
r6901 | slagelwa | 2015-04-06 00:48:46 -0700 (Mon, 06 Apr 2015) | 2 lines
TPP5: If activestate perl is installed deselect and deactivate strawberry perl
r6905 | slagelwa | 2015-04-16 15:43:37 -0700 (Thu, 16 Apr 2015) | 3 lines
Looks like TeamCity may have changed their API. Also put in a error message to tell users when it can't identify the proper file to download.
r6906 | slagelwa | 2015-04-27 00:04:03 -0700 (Mon, 27 Apr 2015) | 2 lines
TPP-5: Added routines for getting the log directory
r6907 | slagelwa | 2015-04-27 00:05:07 -0700 (Mon, 27 Apr 2015) | 2 lines
TPP-5: fixed an issue with getting the current working directory
r6908 | slagelwa | 2015-04-27 00:05:51 -0700 (Mon, 27 Apr 2015) | 2 lines
TPP-5: Not sure why but the win32 components weren't separated correctly
r6909 | slagelwa | 2015-04-28 13:20:32 -0700 (Tue, 28 Apr 2015) | 2 lines
TPP-5: Minor editing of instructions to better reflect the semvar standard
r6911 | slagelwa | 2015-04-30 22:14:27 -0700 (Thu, 30 Apr 2015) | 4 lines
TPP-5: Now with a web server
Fixed some conf/ file issues around web server configuration
r6916 | slagelwa | 2015-05-07 16:10:23 -0700 (Thu, 07 May 2015) | 3 lines
TPP-5: no need to call clean on realclean in boost
fixed license file installation
r6917 | slagelwa | 2015-05-07 22:34:18 -0700 (Thu, 07 May 2015) | 3 lines
TPP-5: Looks like teamcity changed there urls again. Files <> File. Also fixed some undefined warnings.
r6918 | slagelwa | 2015-05-07 23:48:19 -0700 (Thu, 07 May 2015) | 2 lines
these not this
r6919 | slagelwa | 2015-05-08 00:05:56 -0700 (Fri, 08 May 2015) | 4 lines
TPP5 Added back boost-clean to realclean. Its needed
Included version info in boost as I was plyaing
with upgrading it
r6920 | slagelwa | 2015-05-08 00:10:04 -0700 (Fri, 08 May 2015) | 3 lines
TPP5: merged trunch changes from r6824-HEAD
r6921 | slagelwa | 2015-05-08 00:20:07 -0700 (Fri, 08 May 2015) | 2 lines
TPP-5: Make sure readme has windows lines endings
r6922 | slagelwa | 2015-05-08 00:27:18 -0700 (Fri, 08 May 2015) | 2 lines
TPP-5 Updated comet
r6923 | slagelwa | 2015-05-11 22:23:35 -0700 (Mon, 11 May 2015) | 3 lines
TPP-5 appweb was missing license file, oh and cp not mv
the file.
r6924 | slagelwa | 2015-05-11 22:24:45 -0700 (Mon, 11 May 2015) | 3 lines
TPP-5: ignore build and site.mk files
r6927 | slagelwa | 2015-05-13 06:44:12 -0700 (Wed, 13 May 2015) | 2 lines
TPP-5: fixed more security warnings around CGI::param()
r6928 | slagelwa | 2015-05-13 06:45:36 -0700 (Wed, 13 May 2015) | 3 lines
TPP-5: * fixed problems with the windows pwiz programs
* updated windows pwiz to latest build
r6929 | slagelwa | 2015-05-13 23:04:27 -0700 (Wed, 13 May 2015) | 6 lines
TPP-5
* merged trunk r6916:HEAD changes * creates dbase/speclib directory
r6932 | slagelwa | 2015-05-17 22:42:34 -0700 (Sun, 17 May 2015) | 2 lines
TPP-5: fixed a issue introduced by the last merge
r6933 | slagelwa | 2015-05-17 22:43:57 -0700 (Sun, 17 May 2015) | 3 lines
TPP-5: Merged changes from trunk r6694 up to HEAD to address possible missing of changes due to tree conflicts
r6934 | slagelwa | 2015-05-17 23:01:40 -0700 (Sun, 17 May 2015) | 2 lines
TPP-5: fixed issue with bogus message about illegal directory
r6937 | slagelwa | 2015-05-20 12:51:01 -0700 (Wed, 20 May 2015) | 5 lines
TPP-5 Merging r6929 through r6935 from trunk into branch /src
* Mhoopman's fixes * Some proteinprophet change?
r6938 | slagelwa | 2015-05-20 23:11:54 -0700 (Wed, 20 May 2015) | 4 lines
TPP-5:
* Added a warning if users choose not to install appweb or perl * installer/setup comment
r6939 | slagelwa | 2015-05-20 23:14:15 -0700 (Wed, 20 May 2015) | 7 lines
TPP-5:
* noticed there were a few cases where it would try to rebuild the
TPP perl archive when it shouldn't of. So fixed that.
* And thanks, someone took over the SQS CPAN perl module and added a
bunch of tests which cause the build to fail. Others have reported it.
So I specified the version until the *** fixes it.
r6940 | slagelwa | 2015-05-21 00:08:31 -0700 (Thu, 21 May 2015) | 2 lines
TPP-5 mismerge
r6947 | slagelwa | 2015-06-15 23:12:26 -0700 (Mon, 15 Jun 2015) | 2 lines
TPP-5: merged changes from TPP-trunk r6946
r6949 | slagelwa | 2015-06-24 13:12:53 -0700 (Wed, 24 Jun 2015) | 16 lines
TPP-5: Installation now includes licenses for the following:
boost bzip2 d3 expat fann gsl gzstream libarchive libpng libgd
Hopefully this will avoid getting any DMCA's...
r6950 | slagelwa | 2015-06-25 07:51:25 -0700 (Thu, 25 Jun 2015) | 2 lines
TPP-5: Merged Jimmy's latest trunk change
r6951 | slagelwa | 2015-06-25 07:52:38 -0700 (Thu, 25 Jun 2015) | 3 lines
TPP-5: rolled back in the multi_param() calls that probably we removed in
by accident in a merge from trunk
r6952 | slagelwa | 2015-06-25 07:53:06 -0700 (Thu, 25 Jun 2015) | 2 lines
TPP-5: upgraded appeb from 5.4.0 to 6.0.0
r6955 | slagelwa | 2015-07-27 13:10:41 -0700 (Mon, 27 Jul 2015) | 21 lines
TPP-5: Restoring original r6963 change lost by Sourceforge
Revision: 6953 Author: slagelwa Date: 2015-07-16 16:25:49 +0000 (Thu, 16 Jul 2015)
Log Message:
TPP-5: Added/increased timeouts on the petunia script so that multiple jobs finish. The EmbedThis Appweb web server tends to closely watch its threads for requests that might be runaway (for security). Petunia does a fork (or pseudo fork for Windows) then runs using backticks commands for a job. When the first command finishes it appears that Appweb is catching some signal, or at least detects a closing thread then shuts things down. So I've extended the timeouts to match the timeouts being used in Apache (5 hrs). This solves the problem in the short term.
In the long run, we should consider an alternative approach that doesn't use the pseudo-thread model of fork() in perl on Windows. I'd suggest using Win32::Process to create a "real" process, to avoid all of the oddities associated with the web server, both Apache and Appweb...
r6956 | slagelwa | 2015-07-27 13:23:49 -0700 (Mon, 27 Jul 2015) | 16 lines
TPP-5: Restoring original r6964 change lost by Sourceforge
Revision: 6954 Author: slagelwa Date: 2015-07-16 16:28:36 +0000 (Thu, 16 Jul 2015) Log Message:
TPP-5: Reworked checking for ActivePerl including adding a bunch more checks on registry keys. Tested against every installer found in
/proteomics/sw/ActivePerl
As new ActivePerl releases occur they should be added to this folder so we can test against them in the future. (ActivePerl only makes available the most recent and previous release of their product. Older releases are behind a paywall).
r6957 | slagelwa | 2015-07-27 13:27:44 -0700 (Mon, 27 Jul 2015) | 8 lines
TPP-5: Restoring original r6965 change lost by Sourceforge
Revision: 6955 Author: slagelwa Date: 2015-07-16 16:29:35 +0000 (Thu, 16 Jul 2015) Log Message:
TPP-5: cleaned up language in error dialog
r6958 | slagelwa | 2015-07-27 14:37:20 -0700 (Mon, 27 Jul 2015) | 4 lines
TPP-5: Fixed html path in tpp_models.pl. Now uses tpplib function instead of hardcoding it.
r6959 | slagelwa | 2015-07-27 14:38:22 -0700 (Mon, 27 Jul 2015) | 5 lines
TPP-5: Rely on programs just being in PATH in fileDownloader.pl. Can override this if users want by editing file. (I'm not going to go back to using that crazy regex replacing string from the old perl_paths.makefile)
r6960 | slagelwa | 2015-07-27 14:40:46 -0700 (Mon, 27 Jul 2015) | 3 lines
TPP-5: Fixed another multi_param() in tpp_gui with regards to downloading
spec files
r6961 | slagelwa | 2015-07-27 14:43:51 -0700 (Mon, 27 Jul 2015) | 3 lines
TPP-5: added the missing errorbars js file that for some reason was never in
TPP.
r6962 | slagelwa | 2015-07-27 14:58:58 -0700 (Mon, 27 Jul 2015) | 12 lines
TPP-5:
* Fixed issue with perl scripts not running in Petunia by changing the
registry hive from HKCR to HKLM when associating .pl files with the Perl
executable so that it'll work for all users on a system.
* Changed TPP Information to TPP Support in the start menu drop down menu
* Fixed the petunia.ico for shortcuts. Was using a path to the build area
instead of the installation area so it worked fine on dev machines.
r6963 | slagelwa | 2015-07-27 15:02:08 -0700 (Mon, 27 Jul 2015) | 2 lines
TPP-5: Fixed Spectrast ('ST') link in PepXMLViewer
r6964 | slagelwa | 2015-07-27 23:00:02 -0700 (Mon, 27 Jul 2015) | 3 lines
TPP-5 : Fixed ProtXMLViewer/old viewer
r6965 | slagelwa | 2015-07-27 23:02:11 -0700 (Mon, 27 Jul 2015) | 3 lines
TPP-5: added back xsltproc (win32) for protxml viewers
(among other things)
r6966 | slagelwa | 2015-07-29 00:11:22 -0700 (Wed, 29 Jul 2015) | 6 lines
TPP-5: Merging trunk r6947 through r6965 into branch
Two check ins by DSS. Note that these are erronously logged since the SourceForge recovery.
r6967 | slagelwa | 2015-08-04 12:21:44 -0700 (Tue, 04 Aug 2015) | 2 lines
TPP-5: Added back in gnuplot (and now with licenses)
r6968 | slagelwa | 2015-08-04 15:23:10 -0700 (Tue, 04 Aug 2015) | 2 lines
TPP-5: updated comet
r6975 | slagelwa | 2015-08-13 22:21:36 -0700 (Thu, 13 Aug 2015) | 3 lines
TPP-5: Reworked the windows installer one last time to make it simpler to
understand and use.
r6976 | slagelwa | 2015-08-13 23:01:49 -0700 (Thu, 13 Aug 2015) | 15 lines
TPP-5: merge the following changes from trunk to branch
[r6969] by dshteyn InteractParser: add option to record ion_injection_time in
pepXML. Rewrite spectrum names according to TPP conventions.
[r6970] by dshteyn ModificationInfo: BUGFIX, InteractParser was not including variable mods in the peptide string when the listed modifications in the pepXML\ where not in order.
[r6971] by dshteyn mzParser: ionIsolationTime
[r6973] by dshteyn Support legacy calls from Mascot2XML that were breaking the build.
r6977 | slagelwa | 2015-08-13 23:08:54 -0700 (Thu, 13 Aug 2015) | 9 lines
TPP-5: merged following changes from trunk to branch
[r6974] by real_procopio [plot-msms-js] Limit how many scans we backtrack while
looking for parent MS1 scan to 500. Spectra in files with MS2 data only would
take very long to open since the counter was going all the way to the beginning
of the file looking for an MS1 scan.
r6980 | slagelwa | 2015-08-14 12:23:38 -0700 (Fri, 14 Aug 2015) | 2 lines
TPP-5: Fixed some clean and target related issues
r6981 | slagelwa | 2015-08-14 12:26:16 -0700 (Fri, 14 Aug 2015) | 8 lines
TPP-5: Merged in Henry's recent spectrast change:
[r6972] Multi-threading for mz(X)ML search; LINUX standalone compile now uses
mzParser instead of ramp; Decoy ratio analysis now optional
* Also had to fix a cast from int to void pointer warning/error
r6982 | slagelwa | 2015-08-14 13:12:19 -0700 (Fri, 14 Aug 2015) | 9 lines
TPP-5: Merged following changes from trunk into branch:
[6979] PTMProphet: new feature, neutral losses! Changes in modification
specification on commandline!
[6978] PTMProphet: new feature, neutral losses! Changes in modification
specification on commandline
r6983 | slagelwa | 2015-08-14 13:23:12 -0700 (Fri, 14 Aug 2015) | 3 lines
TPP-5: Merging rest of r6966 through r6982 trunk into branch
r6984 | slagelwa | 2015-08-15 20:37:21 -0700 (Sat, 15 Aug 2015) | 7 lines
TPP-5: Having problems linking with gcc on linux. Not sure while, was having similar issue on windows but that was likely a old library issue that I fixed. If anyone knows why the function definition with defaults aren't working please fix.
r6992 | slagelwa | 2015-08-21 12:51:47 -0700 (Fri, 21 Aug 2015) | 2 lines
TPP-5: found some more missing "multi_param()" calls
r6993 | slagelwa | 2015-08-24 23:20:16 -0700 (Mon, 24 Aug 2015) | 2 lines
TPP-5: remerged Henry's changes
r6994 | slagelwa | 2015-08-24 23:23:37 -0700 (Mon, 24 Aug 2015) | 3 lines
TPP-5: added the inno dependency installer so next time Luis installs on a new laptop msconvert will work when he forgets to install its dependencies
r6995 | slagelwa | 2015-08-24 23:48:42 -0700 (Mon, 24 Aug 2015) | 5 lines
TPP-5: Merging trunk r6983 through r6994
* PTMProphet changes
r6998 | slagelwa | 2015-08-25 16:42:13 -0700 (Tue, 25 Aug 2015) | 2 lines
TPP-5: fixed an issue with output paths in jobs
r7007 | slagelwa | 2015-08-30 22:59:49 -0700 (Sun, 30 Aug 2015) | 7 lines
TPP-5: made installing pwiz dependencies an selectable option in the installer as luis found out that sometimes the dependencies can fail to install and this causes the installer to fail. Only option is to then choose not to install pwiz. So now if it fails you can skip installing the dependencies and fix it manually if you really need them.
r7008 | slagelwa | 2015-08-31 08:04:44 -0700 (Mon, 31 Aug 2015) | 2 lines
TPP-5: bumped version
r7009 | slagelwa | 2015-08-31 08:10:52 -0700 (Mon, 31 Aug 2015) | 18 lines
TPP-5: Web server differences
* Apparently not all web servers ignore the exit code of a cgi program. This cgi was one of the rare cases in TPP where a program would exit with a nonzero exit code on an error. Unfortunately in web servers like appweb this means you get a http 502 "Bad Gateway" error returned to the client. So every place were we print a "html" like message, the footer, then exit with non-zero I changed to exit with 0.
In cases where it is a "real" error that doesn't return a complete html page it now prints a message to both stderr and stdout and then exits with a non-zero error code.
* Missing the QUERY_STRING is now no longer an error. Apache probably
provides an empty QUERY_STRING env variable. Appweb doesn't provide one
at all if no parameters provided.
r7010 | slagelwa | 2015-08-31 12:50:21 -0700 (Mon, 31 Aug 2015) | 2 lines
TPP-5: multi_param() again
r7011 | slagelwa | 2015-08-31 13:09:52 -0700 (Mon, 31 Aug 2015) | 2 lines
TPP-5: Fixing path to url transformation
r7014 | slagelwa | 2015-09-02 00:01:26 -0700 (Wed, 02 Sep 2015) | 3 lines
TPP-5: Merged r6995 through r7011 from trunk to this branch
r7015 | slagelwa | 2015-09-02 14:47:13 -0700 (Wed, 02 Sep 2015) | 3 lines
TPP-5: Merged r6995 through r7011 from trunk to branch
(Latest DDS changes)
r7016 | slagelwa | 2015-09-02 22:51:11 -0700 (Wed, 02 Sep 2015) | 3 lines
TPP-5: added urlencode() function to encode cgi parameters then added calls
to encode parameters in PepXMLViewer
r7017 | slagelwa | 2015-09-02 23:32:06 -0700 (Wed, 02 Sep 2015) | 11 lines
TPP-5:
* fixed url to d3.js so it now uses the util function instead of hardcoded url * fixed malformed html document (missing <html> header) * added utf-8 to script line that loads d3.js, since it does have some unicode characters in it that cause javascript errors * commented out the cerr message about parsing. For some reason in appweb this is going to stdout. A normal fprintf(stderr) however doesn't. Odd
r7018 | slagelwa | 2015-09-03 00:09:34 -0700 (Thu, 03 Sep 2015) | 3 lines
TPP-5: Commented out line that was throwing lots of javascript errors. looks
to be unneeded anyhow?
r7019 | slagelwa | 2015-09-03 00:41:08 -0700 (Thu, 03 Sep 2015) | 2 lines
TPP-5: gnuplot.exe set to wgnuplot.exe for Windows
r7020 | slagelwa | 2015-09-04 23:09:26 -0700 (Fri, 04 Sep 2015) | 5 lines
TPP-5:
* improved documentation on path/url functions
* added two new functions for translating paths to urls and back. Meant
to replace the unorthodox mechanisms already in place
r7021 | slagelwa | 2015-09-04 23:10:49 -0700 (Fri, 04 Sep 2015) | 4 lines
TPP-5:
* fixed issue with links being bad to pep3d image when saving as html * took out the now deprecated cygwin and relative #define code sections
r7022 | slagelwa | 2015-09-04 23:54:02 -0700 (Fri, 04 Sep 2015) | 2 lines
TPP-5: fixed spectrast spectrum plot link
r7023 | slagelwa | 2015-09-05 21:55:12 -0700 (Sat, 05 Sep 2015) | 5 lines
TPP-5:
* Add common's path/url conversion functions * Make sure PATH and TPP_HOME are set in tests
r7024 | slagelwa | 2015-09-05 21:56:45 -0700 (Sat, 05 Sep 2015) | 2 lines
TPP-5: make sure our perl is in front of path when testing, for windows
r7025 | slagelwa | 2015-09-05 21:57:37 -0700 (Sat, 05 Sep 2015) | 2 lines
TPP-5: damn typo
r7026 | slagelwa | 2015-09-05 21:58:58 -0700 (Sat, 05 Sep 2015) | 6 lines
TPP-5:
* fixed png path 2 url
* took out all of the cygwin stuff, no longer needed
* took out all the hardcoding of the xslt path. now can have trust the
environment's PATH
r7027 | slagelwa | 2015-09-05 22:32:21 -0700 (Sat, 05 Sep 2015) | 6 lines
TPP-5:
* added missing protein prophet image * fixed path to url conversion * took out old hardcoding of xslt paths * took out old cygwin/WEBSERVER stuff
r7028 | slagelwa | 2015-09-05 23:00:39 -0700 (Sat, 05 Sep 2015) | 2 lines
TPP-5: fixed missing help links on legacy protein prophet viewer
r7029 | slagelwa | 2015-09-06 10:45:32 -0700 (Sun, 06 Sep 2015) | 2 lines
TPP-5: Fixed xslt paths, took out old cgywin/relative webserver stuff
r7030 | slagelwa | 2015-09-06 11:02:01 -0700 (Sun, 06 Sep 2015) | 2 lines
TPP-5: removed extra '/' if present
r7031 | slagelwa | 2015-09-06 11:24:37 -0700 (Sun, 06 Sep 2015) | 3 lines
TPP-5: added a perl-realclean target and fixed an issue on windows were a perl
backup file is required
r7032 | slagelwa | 2015-09-06 11:53:44 -0700 (Sun, 06 Sep 2015) | 2 lines
TPP-5: fixed removing files from processing
r7033 | slagelwa | 2015-09-06 12:00:31 -0700 (Sun, 06 Sep 2015) | 5 lines
TPP-5: fixed new viewer doesn't display anything in pepxmlviewer when a
peptide is clicked on (no peptides shown in view) by merging r6912
trunk changes
r7034 | slagelwa | 2015-09-06 13:40:57 -0700 (Sun, 06 Sep 2015) | 4 lines
TPP-5:
* moved html/ directory creation into html/Makefile * Fixed ProteoGrapher issues
r7041 | slagelwa | 2015-09-10 21:53:04 -0700 (Thu, 10 Sep 2015) | 3 lines
TPP-5: urlencoded another path, this one to the spectrum viewer on comet
results
r7042 | slagelwa | 2015-09-10 22:00:24 -0700 (Thu, 10 Sep 2015) | 3 lines
TPP-5: fixed issue in the top 5 peptides view of comet where the ions url was
bad
r7043 | slagelwa | 2015-09-10 22:12:08 -0700 (Thu, 10 Sep 2015) | 4 lines
TPP-5:
* URL is encoded now from pepxmlviewer, need to decode the parameters * No need to encode the query string as it already is now
r7050 | slagelwa | 2015-09-17 13:22:55 -0700 (Thu, 17 Sep 2015) | 2 lines
TPP-5: updated appweb from 6.0.0 to 6.0.3
r7058 | slagelwa | 2015-10-05 14:34:41 -0700 (Mon, 05 Oct 2015) | 2 lines
TPP-5: updated comet to 2015021
r7069 | slagelwa | 2015-10-16 16:28:13 -0700 (Fri, 16 Oct 2015) | 4 lines
TPP-5: fixed ASAP ratio display problem by commenting out unimplemented mzParser function and exiting with a zero status instead of always returning with a nonzero status.
r7070 | slagelwa | 2015-10-16 17:26:30 -0700 (Fri, 16 Oct 2015) | 2 lines
TPP-5: updated to comet version 2015022
r7077 | slagelwa | 2015-10-21 00:20:18 -0700 (Wed, 21 Oct 2015) | 39 lines
TPP-5: Replaced appweb with apache
While I really wanted to use an smaller footprint, secure, embedded web server (and Luis agreed) and I was almost there besides two last issues, both "arguably non-standard". The first is that stderr and stdout go back to the browser, the second had to do with form proesssings. So at the end of the day
it was easier to revert to using an 3rd party apache build. It at least means
that the commands/user directions are going to be much similar.
I was however able to leverage some of the work done with appweb including (and also note the differences):
1) Its part of the installation (and TPP, under tpp/apache) when installed.
This means it doesn't launch another installer, show up in the programs
folder, or any of that other stuff. Also means it gets removed when
TPP gets removed.
2) Installs a "TPP Apache Web Service" instead of a generic "Apache
Web Service". Nice to see it in the list of services as "TPP".
3) Instead of using the ApacheMonitor I was still able to use the TPP tray
application. (And I changed this to a .bat file to run better from the
command shell). The tray app brands it a little more as tpp, and has
some special menu items specific for tpp, such as opening the web
browser, the data directory, the log directory.
4) Only localhost access is allowed by default. That can be changed of
course by editing the conf files. I guess one could add this as an
option to the installer (and the TPP tray) down the road.
5) It is using the latest 2.2 release of Apache. I tried 2.4, but there are
some conf file directives that changed and aren't backward compatible.
6) Apache log files are under TPP, with the other TPP log files. Users
won't have to hunt them down in Program Files anymore. In fact they can
open it up pretty easily using the TPP tray.
r7078 | slagelwa | 2015-10-21 06:40:09 -0700 (Wed, 21 Oct 2015) | 4 lines
TPP-5: Changed default value of data directory so that if TPP >= 5 was installed
it defaults to its setting of TPP_DATADIR, otherwise if it detects
the old ISB data directory it uses it.
r7079 | slagelwa | 2015-10-21 06:59:36 -0700 (Wed, 21 Oct 2015) | 4 lines
TPP-5: * updated error message if no Apache service
* "primed" the about dialog so it appears on the first click and not
the second
r7080 | mhoopmann | 2015-10-21 11:12:25 -0700 (Wed, 21 Oct 2015) | 4 lines
Adding StPeter to TPP5. It is a tool for computing normalized spectral indexes for proteins, and writing them to the protXML files.
Also updated the Makefile to compile StPeter. IT WAS SOOOO EASY!!!! The new TPP5 is the BEST!!!! Someone else will have to figure out how to put this into TPP4. #nogoingback
r7082 | mhoopmann | 2015-10-21 13:08:57 -0700 (Wed, 21 Oct 2015) | 3 lines
Minor bugfixes when reporting proteins with null or nearly null abundance.
r7085 | mhoopmann | 2015-10-21 15:39:28 -0700 (Wed, 21 Oct 2015) | 3 lines
Increased verbosity for users. Added some progress meters to spectral extraction.
r7086 | slagelwa | 2015-10-21 22:13:08 -0700 (Wed, 21 Oct 2015) | 2 lines
TPP-5: bump build
r7087 | slagelwa | 2015-10-21 22:13:44 -0700 (Wed, 21 Oct 2015) | 2 lines
TPP-5: hack to make tpp_gui.pl backward compatible with old CGI.pm
r7088 | slagelwa | 2015-10-22 16:31:33 -0700 (Thu, 22 Oct 2015) | 2 lines
TPP-5: really only need one conf file now
r7094 | slagelwa | 2015-10-27 16:37:51 -0700 (Tue, 27 Oct 2015) | 2 lines
TPP-5: file was missed in the commit that merged two conf files
r7096 | dshteyn | 2015-10-28 10:20:05 -0700 (Wed, 28 Oct 2015) | 1 line
msys64/mingw64 build tweaks for TPP-5...also adding dependencies for new DISCO features
r7097 | dshteyn | 2015-10-28 11:28:53 -0700 (Wed, 28 Oct 2015) | 1 line
Remove //c flag which was preventing the installer target from finishing
r7103 | dshteyn | 2015-10-30 16:42:32 -0700 (Fri, 30 Oct 2015) | 1 line
Fixing tpp5 build under linux
r7104 | mhoopmann | 2015-11-16 12:28:24 -0800 (Mon, 16 Nov 2015) | 3 lines
Updated parser to handle many malformed modification masses produced by various search engines. Check for input files in CWD if paths in the prot.xml and pep.xml files are broken. Also exporting results in MsStats format, at least temporarily.
r7107 | mhoopmann | 2015-11-16 15:28:34 -0800 (Mon, 16 Nov 2015) | 3 lines
Jason's modifications to optionally export non-normalized peptide intensities.
r7108 | mhoopmann | 2015-11-16 15:44:51 -0800 (Mon, 16 Nov 2015) | 3 lines
Quick bugfix to correct output.
r7109 | mhoopmann | 2015-11-16 15:52:39 -0800 (Mon, 16 Nov 2015) | 3 lines
More bugfixes: export normalized SI values now.
r7110 | mhoopmann | 2015-11-16 17:06:33 -0800 (Mon, 16 Nov 2015) | 3 lines
Code cleanup and fix when reporting SIn to external file (not the ProtXML)
r7114 | mhoopmann | 2015-12-02 12:01:06 -0800 (Wed, 02 Dec 2015) | 3 lines
Added additional modification masses and fixed a typi (heh) in the usage statement.
r7115 | mhoopmann | 2015-12-02 12:08:37 -0800 (Wed, 02 Dec 2015) | 3 lines
Forgot to update the headers. This has now been remedied.
r7123 | dshteyn | 2015-12-29 12:27:59 -0800 (Tue, 29 Dec 2015) | 1 line
Merge fix from trunk
r7131 | dshteyn | 2016-01-04 15:25:43 -0800 (Mon, 04 Jan 2016) | 1 line
libgd MingW64 build
r7132 | dshteyn | 2016-01-04 15:48:26 -0800 (Mon, 04 Jan 2016) | 1 line
Correct message text
r7133 | dshteyn | 2016-01-04 16:27:30 -0800 (Mon, 04 Jan 2016) | 1 line
MSYS2 build instructions
r7134 | dshteyn | 2016-01-05 13:00:24 -0800 (Tue, 05 Jan 2016) | 1 line
BUGFIX: RespectParser fixed a problem which caused Neutral Loss use to significantly hinder running times.
r7135 | dshteyn | 2016-01-05 13:02:20 -0800 (Tue, 05 Jan 2016) | 1 line
Missing character in Makefile was causing the build to crash when building GZSTREAM
r7136 | slagelwa | 2016-01-07 14:33:24 -0800 (Thu, 07 Jan 2016) | 3 lines
TPP-5: provide a more meanful and correct error message if tpp_hostname
can't be invoked
r7137 | slagelwa | 2016-01-07 14:36:01 -0800 (Thu, 07 Jan 2016) | 2 lines
TPP-5: fix case where 2010 gets installed twice. (UNTESTED)
r7138 | slagelwa | 2016-01-08 10:45:00 -0800 (Fri, 08 Jan 2016) | 4 lines
TPP-5: use Digest::MD5 (found in Perl core) to calculate MD5 checksums instead of invoking the md5sum program. Much, much more efficent and doesn't risk sutble platform nuances.
r7139 | dshteyn | 2016-01-08 14:53:48 -0800 (Fri, 08 Jan 2016) | 1 line
BUGFIX vcredist2010
r7140 | dshteyn | 2016-01-10 20:31:39 -0800 (Sun, 10 Jan 2016) | 1 line
Check Path for C:\Windows\System32 (for cmd.exe) and add if missing
r7141 | dshteyn | 2016-01-10 20:41:58 -0800 (Sun, 10 Jan 2016) | 1 line
bump version
r7142 | dshteyn | 2016-01-12 13:57:47 -0800 (Tue, 12 Jan 2016) | 1 line
BUGFIX: UAC runas admin enabled allows the tray to control the apache, wperl gets the empty command prompt to go away
r7143 | dshteyn | 2016-01-12 14:04:15 -0800 (Tue, 12 Jan 2016) | 1 line
reduce verbose level
r7144 | slagelwa | 2016-01-13 12:06:40 -0800 (Wed, 13 Jan 2016) | 2 lines
TPP-5: Cleaned up Apache instructions
r7145 | dshteyn | 2016-01-13 15:50:13 -0800 (Wed, 13 Jan 2016) | 1 line
Added port control to installer. https replaced with http. Install favicon.ico.
r7146 | dshteyn | 2016-01-13 16:56:05 -0800 (Wed, 13 Jan 2016) | 1 line
New target configure will configure the installation by setting the values in httpd-tpp.conf to the TPP defaults defined in common.mk.
r7147 | dshteyn | 2016-01-14 21:47:13 -0800 (Thu, 14 Jan 2016) | 1 line
Makefile targets: configure and start to configure and launch new installation non-interactively, environment variables PATH must include a path to perl TPP_HOME must be setup manually for the TPP to work
r7148 | dshteyn | 2016-01-15 12:33:55 -0800 (Fri, 15 Jan 2016) | 1 line
Added makefile targets to install / uninstall and control the TPP through make alone...should help with automated building on windows
r7149 | dshteyn | 2016-01-15 21:34:47 -0800 (Fri, 15 Jan 2016) | 1 line
Use the Inno /silent feature to run the installer non-interactively. Removed the makefile changes to have one place of control for installation in the Inno setup tool.
r7150 | dshteyn | 2016-01-16 15:26:08 -0800 (Sat, 16 Jan 2016) | 1 line
Bump version
r7151 | dshteyn | 2016-01-16 21:07:08 -0800 (Sat, 16 Jan 2016) | 1 line
Adjust Makefile to improve get make installer to function...was breaking on schema
r7152 | dshteyn | 2016-01-17 17:53:36 -0800 (Sun, 17 Jan 2016) | 1 line
Fix more make installer problems ...
r7153 | dshteyn | 2016-01-18 11:51:04 -0800 (Mon, 18 Jan 2016) | 1 line
Adjust usage statement in makefile and UAC vbs script that was failing on win 7
r7154 | dshteyn | 2016-01-19 10:28:03 -0800 (Tue, 19 Jan 2016) | 1 line
Adjust components to uninstall
r7155 | dshteyn | 2016-01-19 16:28:16 -0800 (Tue, 19 Jan 2016) | 3 lines
make installer configuration tweaks..pull getUAC.bat as a separate script for make can utilize it for installation
r7156 | dshteyn | 2016-01-19 22:18:00 -0800 (Tue, 19 Jan 2016) | 1 line
Allow svn revision to be included in "exported" builds
r7157 | dshteyn | 2016-01-19 22:18:54 -0800 (Tue, 19 Jan 2016) | 1 line
bump version
r7158 | dshteyn | 2016-01-20 10:05:42 -0800 (Wed, 20 Jan 2016) | 1 line
Update comet version
r7159 | dshteyn | 2016-01-20 15:46:38 -0800 (Wed, 20 Jan 2016) | 1 line
PeptideMapper tool
r7160 | dshteyn | 2016-01-20 15:54:20 -0800 (Wed, 20 Jan 2016) | 1 line
Install parameters
r7161 | dshteyn | 2016-01-20 16:57:18 -0800 (Wed, 20 Jan 2016) | 1 line
Install PeptideMapper
r7162 | dshteyn | 2016-01-21 14:29:17 -0800 (Thu, 21 Jan 2016) | 1 line
Change uninstall target to wait for uninstaller to finish (up to 5 mins)...was failing at uninstall target on Win 7...bump version
r7163 | real_procopio | 2016-01-21 17:05:03 -0800 (Thu, 21 Jan 2016) | 1 line
Add Hardklor target to Linux build
r7164 | slagelwa | 2016-01-21 17:35:57 -0800 (Thu, 21 Jan 2016) | 3 lines
TPP-5: added other part to make sure hardklor gets installed on both
platforms
r7165 | slagelwa | 2016-01-21 22:21:04 -0800 (Thu, 21 Jan 2016) | 2 lines
TPP-5: cache results of calls to tpp_hostname
r7166 | slagelwa | 2016-01-22 10:54:13 -0800 (Fri, 22 Jan 2016) | 13 lines
TPP5:
* Added realclean targets for mstoolkit and hardklor so top level
realclean doesn't fail
* Reworked rule for hardklor so that its a phony target and depends
on the actual files made. That way it doesn't run every time.
* Reworked rules for mstookkit so that its a phony target and depends
on the actual files made. That way it doesn't run every time.
* Removed mstoolkit dependency from hardklor so you can run make hardklor
in its diretory. Assumes that the library exists and was made for
you. Did however add a dependency for it at the higher level to
make sure it gets made first. Dependencies are a b*tch.
r7167 | real_procopio | 2016-01-22 13:50:44 -0800 (Fri, 22 Jan 2016) | 1 line
[PepXMLViewer] Do not show start_scan column by default; remove old commented-out code
r7168 | dshteyn | 2016-01-22 18:03:19 -0800 (Fri, 22 Jan 2016) | 1 line
quotes were creating a problem ...
r7169 | dshteyn | 2016-01-22 18:24:41 -0800 (Fri, 22 Jan 2016) | 1 line
Change the batch scripts to work whether the path given is quoted (called from Windows CMD) or not (called from MinGW shell)...
r7170 | dshteyn | 2016-01-25 11:05:54 -0800 (Mon, 25 Jan 2016) | 1 line
New comet version
r7171 | slagelwa | 2016-01-25 14:02:03 -0800 (Mon, 25 Jan 2016) | 3 lines
TPP-5: Fixed the circular dependency issue with the dependencies
r7172 | slagelwa | 2016-01-26 12:28:06 -0800 (Tue, 26 Jan 2016) | 2 lines
TPP-5: lets not configure boost for mingw on linux systems
r7173 | slagelwa | 2016-01-26 12:45:01 -0800 (Tue, 26 Jan 2016) | 3 lines
TPP-5: Move the directory order-only preq on the targets that are actually
in the directory. Otherwise it doesn't get run when needed.
r7174 | real_procopio | 2016-01-26 14:23:37 -0800 (Tue, 26 Jan 2016) | 1 line
[comet-pepxml.cgi] Add support for cases when mz data file is in different directory than pepXML file: extract mzML filename from pepXML msms_run_summary tag, go back to old behavior if file is not found; update link to Lorikeet by passing mzML file, scan number, and charge; added a spectrum name parsing sub; minor code clean-up to ensure proper xml attribute is collected
r7175 | dshteyn | 2016-01-26 16:35:02 -0800 (Tue, 26 Jan 2016) | 1 line
Compilation was getting stuck on MSSingleScan due to target order...fixed
r7176 | real_procopio | 2016-01-26 17:00:39 -0800 (Tue, 26 Jan 2016) | 1 line
[plot-msms-js] Added fake data points to force Lorikeet to always scale [0-2000], unless there is data beyond this range; updated link to project page
r7177 | dshteyn | 2016-01-27 10:40:19 -0800 (Wed, 27 Jan 2016) | 1 line
Remove unused variable breaking build on linux
r7178 | dshteyn | 2016-01-27 10:41:42 -0800 (Wed, 27 Jan 2016) | 1 line
Remove circular dependency
r7179 | real_procopio | 2016-01-27 13:17:45 -0800 (Wed, 27 Jan 2016) | 1 line
Remove unused file
r7180 | dshteyn | 2016-01-27 16:07:52 -0800 (Wed, 27 Jan 2016) | 1 line
Simplify TPPVersion setting...report the build time and svn revision...remove nonessential obfuscation
r7181 | dshteyn | 2016-01-28 10:15:14 -0800 (Thu, 28 Jan 2016) | 1 line
Fix typo...bump version
r7182 | real_procopio | 2016-01-28 13:12:16 -0800 (Thu, 28 Jan 2016) | 1 line
[RefreshParser] Show header of troublesome sequence entry when it is too large for processing; also re-tabbed code for readability
r7183 | real_procopio | 2016-01-28 13:13:27 -0800 (Thu, 28 Jan 2016) | 1 line
[RefreshParser] Show header of troublesome sequence entry when it is too large for processing; also re-tabbed code for readability
r7184 | real_procopio | 2016-01-28 17:25:46 -0800 (Thu, 28 Jan 2016) | 1 line
[TPP Models] Capture St.Peter analysis summary values; minor JS code cleanup
r7185 | dshteyn | 2016-02-08 16:37:08 -0800 (Mon, 08 Feb 2016) | 3 lines
BUGFIX compareProts.pl: fix issues with creating the d3 file for comparing protein lists. BUGFIX in the interaction with 2-list protein comparison (mouseovers were enabling the wrong protein display, now fixed)
tpp_gui : Petunia changes towards a refreshed color scheme
r7186 | real_procopio | 2016-02-08 16:41:54 -0800 (Mon, 08 Feb 2016) | 1 line
[ProtProphModels] Use non-POSIX time string (for Windows compatibility); display location of xml being changed to user
r7187 | dshteyn | 2016-02-09 11:29:23 -0800 (Tue, 09 Feb 2016) | 1 line
BUGFIX: set the TPP_BUILDID in one place the common.mk file and incorporate the svn revision and build time once...this allows make version to work and set the time and revision instead of xxxx-xxxx
r7188 | dshteyn | 2016-02-10 20:11:24 -0800 (Wed, 10 Feb 2016) | 1 line
Warn the user if a previous installation is detected, but pose a question if they'd like to continue. TPP 5 seems to live ok with pre-5 TPP in tests so far....more testing needed
r7189 | real_procopio | 2016-02-17 15:14:45 -0800 (Wed, 17 Feb 2016) | 1 line
[ProtProphetModels] Always use Unix EOL, even in Windows (files are produced that way in TPP)
r7190 | slagelwa | 2016-02-18 10:17:25 -0800 (Thu, 18 Feb 2016) | 2 lines
TPP-5: added zip/unzip dependencies
r7191 | real_procopio | 2016-02-18 17:08:41 -0800 (Thu, 18 Feb 2016) | 1 line
[ProtProphetModels] Report calculated decoy ratio; remove unneeded declaration
r7192 | real_procopio | 2016-02-18 18:00:46 -0800 (Thu, 18 Feb 2016) | 9 lines
[ProtXMLViewer]
- Added support for StPeter quantitation results
- Added ability to sort peptides
- View quant ratios as either numerical (with errors) or graphical bars
- Added basic spectrum stats for XPRESS results
- Show peptide map graphic when viewing shared peptides via the weight link
- Add peptides to exported TSV results (and change default file extension to .tsv)
- Turn off warnings for CGI parameters passed as a list
r7194 | real_procopio | 2016-02-23 16:12:04 -0800 (Tue, 23 Feb 2016) | 8 lines
[plot-msms-js] Added support for multiple (up to 5) side-by-side Lorikeet instances, with tab-switching - Still uses same base spectrum, so best use is to compare multiple interpretations of same spectrum - Handles charges, sequences, and all modifications independently of each other - Fully backwards-compatible; usage for first/single peptide is unchanged
URL usage for extra peptides: PepA=PEPTIDESEQ&ChargeA=2&ModA4=147.035&PepB=ANOTHERPEPTIDE&ChargeB=3&ModBC=45.1433 Peptides are designated A-D, last element above shows C-term mod on peptide B
r7196 | real_procopio | 2016-02-24 14:50:48 -0800 (Wed, 24 Feb 2016) | 7 lines
[comet-pepxml]
- Proof-of-concept: added link to view top hits (up to 5) in tabbed Lorikeet
Also:
- Fixed bug where bad comparison of mass_type ("average") strings resulted in incorrect url param
- Added page title and html footer with TPP version
- Minor code changes to building spectrum link; no net user effect.
r7197 | real_procopio | 2016-02-24 14:54:06 -0800 (Wed, 24 Feb 2016) | 1 line
[plot-msms-js] Added user-defined tab labels (default = peptide sequence)
r7199 | real_procopio | 2016-02-24 17:12:11 -0800 (Wed, 24 Feb 2016) | 1 line
[plot-msms-js] Added animation (slow/fast) with dynamic user selection; added utility function for printing tabs
r7200 | real_procopio | 2016-02-24 17:48:11 -0800 (Wed, 24 Feb 2016) | 1 line
[plot-msms-js] Make sure we can still display uninterpreted spectra -- e.g. from Pep3D
r7201 | real_procopio | 2016-02-25 18:39:26 -0800 (Thu, 25 Feb 2016) | 1 line
[Lorikeet] Update to lastest available version (Sep 2015)
r7202 | real_procopio | 2016-02-25 19:05:28 -0800 (Thu, 25 Feb 2016) | 1 line
[plot-msms-js] Handle fragment mass error and pass it to Lorikeet, via URL parameter 'MassError'
r7203 | dshteyn | 2016-02-29 15:38:57 -0800 (Mon, 29 Feb 2016) | 1 line
PTMProphet, RTCatalog, RTCalculator, SpectraST: check in the latest code.
r7204 | dshteyn | 2016-02-29 15:44:45 -0800 (Mon, 29 Feb 2016) | 1 line
tpp_gui: Default debug off
r7205 | real_procopio | 2016-02-29 15:57:39 -0800 (Mon, 29 Feb 2016) | 4 lines
[ASAPRatioPeptideParser]
- Added progress bar
- Display exe name and version at launch
- Cleaned up (some) code formatting and removed (some) unused code
r7206 | real_procopio | 2016-02-29 16:24:35 -0800 (Mon, 29 Feb 2016) | 1 line
[ProtXMLViewer] Fix link to models page in Windows by making drive letter comparison case-insensitive (as is Windows, brilliantly...)
r7207 | real_procopio | 2016-02-29 16:27:13 -0800 (Mon, 29 Feb 2016) | 1 line
[ProtXMLViewer] Tied to previous check-in -- replace text in actual filename being tested...oops
r7208 | real_procopio | 2016-02-29 16:28:44 -0800 (Mon, 29 Feb 2016) | 1 line
[ProtXMLViewer] Tied to previous 2 check-ins -- third time's a charm! Ugh.
r7209 | dshteyn | 2016-02-29 17:05:27 -0800 (Mon, 29 Feb 2016) | 1 line
Comment out DEBUG=1 for now since building with DEBUG flags in mingw-64 msys2 causes g++ to error out with "Fatal error: can't close file too big" when building Pwiz.
r7210 | dshteyn | 2016-02-29 17:27:20 -0800 (Mon, 29 Feb 2016) | 1 line
SpectraST: new code from branch
r7211 | dshteyn | 2016-03-01 10:52:55 -0800 (Tue, 01 Mar 2016) | 1 line
SpectraST: merging new code from trunk.
r7212 | slagelwa | 2016-03-01 23:09:11 -0800 (Tue, 01 Mar 2016) | 6 lines
TPP-5
* renamed depinstaller to innodependencyinstaller to faciliate updates and use
the name it gets cloned out of git as
* touched up the installer make rules
r7213 | slagelwa | 2016-03-02 00:17:05 -0800 (Wed, 02 Mar 2016) | 7 lines
TPP-5:
* removed commented out include line, doesn't work/isn't needed * updated to latest inno dependency installer * updated to use .Net 4.6, seems to solve the 4.5 failure problem * added some instructions on how to update using git
r7214 | dshteyn | 2016-03-02 10:36:44 -0800 (Wed, 02 Mar 2016) | 1 line
Append TPP paths to the front of PATH
r7215 | real_procopio | 2016-03-02 14:29:05 -0800 (Wed, 02 Mar 2016) | 1 line
[decoy models] Integrate pep- and i- prophets decoy validation analysis into pepXML and into the models page. For old usage, use the -G (gnuplot only) command-line option
r7216 | real_procopio | 2016-03-03 11:13:32 -0800 (Thu, 03 Mar 2016) | 1 line
[ProphetModels] Fix Windows-related line ending issue
r7217 | dshteyn | 2016-03-07 15:57:42 -0800 (Mon, 07 Mar 2016) | 1 line
Point to the correct path for protxml2html.pl
r7218 | real_procopio | 2016-03-10 11:48:04 -0800 (Thu, 10 Mar 2016) | 1 line
[ProtXMLViewer] Render Libra ratios as vertical blue bars by default (instead of horizontal color bars); also added heatmap-like option
r7219 | real_procopio | 2016-03-11 14:30:06 -0800 (Fri, 11 Mar 2016) | 1 line
[ProtXMLViewer] Fix Excel (tsv) export when including all peptides; added link to download resulting file post-export
r7220 | real_procopio | 2016-03-11 16:04:07 -0800 (Fri, 11 Mar 2016) | 1 line
[ProtXMLViewer] Fix sorting for very large sub-groups (that go past "az")
r7221 | dshteyn | 2016-03-14 14:17:56 -0700 (Mon, 14 Mar 2016) | 1 line
Adjust the alias to allow plotspectrast.cgi to correctly reference the butterfly plot image ...
r7222 | dshteyn | 2016-03-14 14:20:03 -0700 (Mon, 14 Mar 2016) | 1 line
SpectraST: Fix some problems with SpectraST...including proton mass reference, plotspectrast.cgi image reference, initialize rtLandmarks to NULL, etc...
r7223 | dshteyn | 2016-03-14 14:20:49 -0700 (Mon, 14 Mar 2016) | 1 line
PTMProphet: make fixes associated with MASSDIFFMODE analysis for SpectraST open-mod searching
r7224 | slagelwa | 2016-03-15 12:32:36 -0700 (Tue, 15 Mar 2016) | 2 lines
TPP-5: installer should reuse previous settings if upgrading
r7225 | dshteyn | 2016-03-15 13:10:19 -0700 (Tue, 15 Mar 2016) | 1 line
PTMProphet: Propagate the modifications from the search results when in MASSDIFFMODE
r7226 | real_procopio | 2016-03-16 12:39:14 -0700 (Wed, 16 Mar 2016) | 1 line
[ProteinProphet] Re-teach PP how to compute protein lengths. This has been broken since commit 6856. Also removed some no longer used code
r7227 | real_procopio | 2016-03-16 18:45:03 -0700 (Wed, 16 Mar 2016) | 7 lines
[ProteinProphet] - Generate error vs min_prob table and insert into protXML (similar to the one produced by PeptideProphet) - Write sens/error info into XML by ascending error rate (as in the other prophets) - Stop plotting sens/err png by default; removed NOPLOT option. To produce png, use new PLOTPNG option - Took out even more unused code - Minor code reformatting and spelling correction
r7228 | real_procopio | 2016-03-16 18:45:19 -0700 (Wed, 16 Mar 2016) | 7 lines
[ProteinProphet] - Generate error vs min_prob table and insert into protXML (similar to the one produced by PeptideProphet) - Write sens/error info into XML by ascending error rate (as in the other prophets) - Stop plotting sens/err png by default; removed NOPLOT option. To produce png, use new PLOTPNG option - Took out even more unused code - Minor code reformatting and spelling correction
r7229 | real_procopio | 2016-03-16 18:56:55 -0700 (Wed, 16 Mar 2016) | 5 lines
[tpp_models] - Display new error table from protXML, if present - Add tpp_models run datetime; removed debug tab (still available in DEBUG mode) - Do not display error tables tab if no data - Fixed wrong call to clear hashes
r7230 | real_procopio | 2016-03-17 19:05:22 -0700 (Thu, 17 Mar 2016) | 6 lines
[ProteinProphet] - New progress bars and cleaner, more consistent user feedback - Warn users if protein has any zero-mass residues, and display them with affected sequence - Fix call to Libra (use condition file, not channel number) - Updated and reformatted usage statement
r7231 | real_procopio | 2016-03-18 12:24:35 -0700 (Fri, 18 Mar 2016) | 1 line
[tpp_models] Make sure that the protein error tables appear!
r7232 | real_procopio | 2016-03-23 19:01:56 -0700 (Wed, 23 Mar 2016) | 1 line
[PepXMLViewer] Initial support for cross-linking results (specifically from Kojak) -- display both peptides and both proteins from 'xl' entries, along with their individual scores and overall spectrum search scores; link to (tabbed) Lorikeet with both peptides (had to import AA masses to compute appropriate modified mass at link site
r7233 | real_procopio | 2016-03-24 12:46:44 -0700 (Thu, 24 Mar 2016) | 1 line
[PepXMLViewer] Clean up alignment of various filters and options; added iProphet quick-filter to summary section; expanded size of filename text box; re-indented code in PepXOptions.cpp
r7234 | real_procopio | 2016-03-24 16:56:03 -0700 (Thu, 24 Mar 2016) | 1 line
[PepXMLViewer] Clean up display for quantitation fields and less popular search engines (Myrimatch, OMSSA, MSGF+, etc). Also added ability to format unruly values into decimal or scientific notation
r7235 | real_procopio | 2016-03-25 16:44:16 -0700 (Fri, 25 Mar 2016) | 6 lines
[PepXMLViewer] - Added filter options for KOJAK fields - Moved iProphet probability to first column by default - Added filter options for all iProphet models and cleaned up options - Removed obsolete iProphet fields from possible column list
r7236 | real_procopio | 2016-03-29 14:54:45 -0700 (Tue, 29 Mar 2016) | 1 line
[Petunia] Add St.Peter support and Neutral Losses in PTMProphet
r7237 | real_procopio | 2016-03-30 17:11:43 -0700 (Wed, 30 Mar 2016) | 6 lines
[Petunia] - Add simple interface to Kojak (and Percolator) - Fix 'icon' type in href - Subtly highlight when running a sub-command in command output (e.g. as in xinteract) - Minor code formatting
r7238 | real_procopio | 2016-03-31 18:59:19 -0700 (Thu, 31 Mar 2016) | 1 line
[PepXMLViewer] Added support for PLink and ProteinProspector cross-link results; fixed spectrum link and display of loop-link peptides
r7239 | real_procopio | 2016-03-31 19:30:29 -0700 (Thu, 31 Mar 2016) | 1 line
[PepXMLViewer] Allow NTT filter to have min and max values; also added similar filter for NMC
r7240 | real_procopio | 2016-03-31 19:35:27 -0700 (Thu, 31 Mar 2016) | 1 line
[Petunia] Fix tpp_bin and tpp_gui_url references for Kojak and Percolator
r7241 | slagelwa | 2016-04-06 13:30:07 -0700 (Wed, 06 Apr 2016) | 3 lines
TPP-5: Rewrote parameters rules so they don't run every single time. Also
fixed them so they are updated automatically if the source files change
r7242 | slagelwa | 2016-04-06 14:10:35 -0700 (Wed, 06 Apr 2016) | 2 lines
TPP-5: Doubt we want Proteowizard comment block in the MSToolkit Makefile
r7243 | slagelwa | 2016-04-06 14:14:28 -0700 (Wed, 06 Apr 2016) | 2 lines
TPP-5: removed circular references
r7244 | slagelwa | 2016-04-06 22:34:11 -0700 (Wed, 06 Apr 2016) | 2 lines
TPP-5: can't make dir on a phony target
r7245 | slagelwa | 2016-04-06 22:55:20 -0700 (Wed, 06 Apr 2016) | 5 lines
TPP-5: Sign, resort to using a marker file. It appears that in windows we're using make 4.0, which treats pattern matching slightly differently and hence wasn't working correctly for directories.
r7246 | dshteyn | 2016-04-07 12:41:08 -0700 (Thu, 07 Apr 2016) | 1 line
RTCatalog: updated with more features
r7247 | dshteyn | 2016-04-07 12:42:08 -0700 (Thu, 07 Apr 2016) | 1 line
PTMProphet: updated with more bug fixes and MASSDIFFMODE improvements
r7248 | dshteyn | 2016-04-07 12:43:29 -0700 (Thu, 07 Apr 2016) | 1 line
InteractParser: bug fix spetrum name mangling under certain nativeSpectrumID conditions
r7249 | dshteyn | 2016-04-07 12:45:50 -0700 (Thu, 07 Apr 2016) | 1 line
ProteinProphet: improve warning message and not crash when database file is not where specified.
r7250 | real_procopio | 2016-04-08 14:43:42 -0700 (Fri, 08 Apr 2016) | 1 line
[Petunia] Step 1 of full Look&Feel revamp : simplified and streamlined navigation and menus; some code clean-up. More to do, but fully-functional as-is
r7251 | real_procopio | 2016-04-08 20:31:19 -0700 (Fri, 08 Apr 2016) | 1 line
[Petunia] Step 2 of full L&F revamp: new style for tools sections and submit buttons; highlight selected checkboxes and radio buttons; removed step counts; removed "nter" from interprophet; darkened body background
r7253 | slagelwa | 2016-04-11 16:39:05 -0700 (Mon, 11 Apr 2016) | 2 lines
TPP-5: fix an dependency order issue between libgd and libpng
r7254 | real_procopio | 2016-04-11 20:06:35 -0700 (Mon, 11 Apr 2016) | 1 line
[Petunia] Step 3 of full L&F revamp: consider Kojak a Pipeline Type (and thus not under tools; added dynamic filter to Speclibs page; updated to current ISB logo; removed black borders from all logos; changed page background to white; more css harmonization
r7255 | mhoopmann | 2016-04-12 15:03:13 -0700 (Tue, 12 Apr 2016) | 3 lines
Improved pathfinding for locating mzML files.
r7256 | real_procopio | 2016-04-12 19:42:15 -0700 (Tue, 12 Apr 2016) | 1 line
[Petunia] Step 4 of full L&F revamp: Almost done cleaning up CSS; added basic Comet params editor page (will also be used for kojak.params)
r7257 | slagelwa | 2016-04-12 22:57:33 -0700 (Tue, 12 Apr 2016) | 3 lines
TPP-5: updated process to download ProteoWizard from Team City. Now uses
targets in the Makefile and the "newer" URL API.
r7258 | slagelwa | 2016-04-13 20:30:01 -0700 (Wed, 13 Apr 2016) | 2 lines
TPP-5: can't use MKDIR on a phony target
r7259 | slagelwa | 2016-04-13 20:42:24 -0700 (Wed, 13 Apr 2016) | 2 lines
TPP-5: can't use MKDIR on a phony target
r7260 | slagelwa | 2016-04-15 12:24:26 -0700 (Fri, 15 Apr 2016) | 4 lines
TPP-5: Updated how TPP manages ProteoWizard. No longer keep the Windows dlls
in subversion and instead now just use the installer to install on
Windows.
r7262 | real_procopio | 2016-04-19 14:50:45 -0700 (Tue, 19 Apr 2016) | 8 lines
[Petunia] - Added support for editing Kojak params files - Insert date/time and user info as a comment when saving comet/kojak params via Petunia - Updated menu names for Qualscore, StPeter, and reSpect - Added 'filter files here' hint text to files filter box - Minor code reformatting
r7263 | real_procopio | 2016-04-19 18:56:08 -0700 (Tue, 19 Apr 2016) | 5 lines
[Petunia] - Added ability to choose mzML input file(s) for Kojak - Added Comet and Kojak help link for each search parameter - Added support for TMT-10 in Libra conditions page
r7264 | real_procopio | 2016-04-20 18:01:01 -0700 (Wed, 20 Apr 2016) | 8 lines
[Petunia] - Edited some of the tools descriptions - Show short explanation at the top of each tool page - Use "Specify" and "Choose" in a consistent manner - Decoy Peps and Decoy Prots pages now request specific xml types (pep.xml and prot.xml, respectively) - More formatting tweaks - Removed unused "Resultspage" session setting
r7265 | real_procopio | 2016-04-20 19:39:00 -0700 (Wed, 20 Apr 2016) | 4 lines
[Petunia] - Do not display full jobs list when viewing a specific command output - Partial redesign of jobs page (still a little more to do) - Minor code and page formatting
r7266 | real_procopio | 2016-04-22 17:40:44 -0700 (Fri, 22 Apr 2016) | 1 line
[Petunia] Redesign Jobs page and clean up stylesheet
r7267 | real_procopio | 2016-04-25 13:45:51 -0700 (Mon, 25 Apr 2016) | 5 lines
[Petunia] - Animate button after action is submitted until completion (e.g. Copy/Paste a large file) - Change name of css entry: formentryhead -> tablehead - Fix html on Jobs page - Minor html change on PeptideProphet/decoy parameters
r7268 | real_procopio | 2016-04-25 17:48:37 -0700 (Mon, 25 Apr 2016) | 1 line
[Petunia] Added Disco interface
r7270 | real_procopio | 2016-04-27 14:01:41 -0700 (Wed, 27 Apr 2016) | 1 line
[ProteinProphet] Cleaned up usage statement
r7271 | real_procopio | 2016-04-27 16:57:09 -0700 (Wed, 27 Apr 2016) | 8 lines
[Petunia] - Fix calling Libra via ProteinProphet by including condition file name and cd to output dir - Updated NOPROTLEN option in ProteinProphet call - Do not display 'Kill Command' link in Jobs page once command is finished - Line up TPP tools sub-menus - Spified up login page - Remove obsolete show/hide JS code - Small css tweaks
r7272 | real_procopio | 2016-04-27 19:17:29 -0700 (Wed, 27 Apr 2016) | 1 line
[PepXMLViewer] Display "KScore" as the column heading when viewing XTandem (K-score) results -- which are stored in pepXML as "hyperscore"
r7273 | real_procopio | 2016-04-28 14:54:30 -0700 (Thu, 28 Apr 2016) | 1 line
[Petunia] Remove Marimba! Also clarified idconvert text and rearranged main menu items
r7274 | real_procopio | 2016-04-28 15:44:22 -0700 (Thu, 28 Apr 2016) | 1 line
[Petunia] Spified up Mascot search page: add page size filter, highlight selected file to download, collapse server URL setting if results are returned
r7275 | real_procopio | 2016-04-29 20:51:29 -0700 (Fri, 29 Apr 2016) | 1 line
[PepXMLViewer] Display multiple PTMProphet analysis results for the same spectrum using different colors for each (up to 7 -- for now?)
r7276 | real_procopio | 2016-05-02 13:31:09 -0700 (Mon, 02 May 2016) | 1 line
[PepXMLViewer] Adjust a couple of PTM colors
r7277 | real_procopio | 2016-05-02 16:34:13 -0700 (Mon, 02 May 2016) | 1 line
[Petunia] Added RefreshParser page; Close all other menus when another one is opened; Small text updates
r7278 | eng_jk | 2016-05-03 13:59:40 -0700 (Tue, 03 May 2016) | 2 lines
add option to pass ion series to use in Lorikeet plotting
r7279 | real_procopio | 2016-05-03 15:23:28 -0700 (Tue, 03 May 2016) | 1 line
[Petunia] New blue footer and blue-background images. Added drop shadows to form divs. CSS tweaks
r7280 | real_procopio | 2016-05-04 11:56:16 -0700 (Wed, 04 May 2016) | 1 line
[PepXMLViewer] Pass ions series from search params to Lorikeet; also changed column headers: *** "ions"-->"ions_old" (old viewer), "ions2"-->"ions" (lorikeet) *** ; minor code clean-up
r7281 | real_procopio | 2016-05-04 16:26:42 -0700 (Wed, 04 May 2016) | 1 line
[Libra] Add progress bar; display executable name and version when running; Some code clean-up
r7282 | real_procopio | 2016-05-04 18:27:17 -0700 (Wed, 04 May 2016) | 7 lines
[Petunia] - Only display bubble with number of running/active jobs next to Jobs tab menu title (mouse-over still displays status summary of all jobs) - Add filter box on jobs page - On Libra conditions page, only display m/z of relevant channels when selecting from drop-down; blank out all others - Add visual separator between current directory tree and list of subdirectories in filebrowser/picker - Round corners for messages divs - More css tweaks (shadows!)
r7283 | real_procopio | 2016-05-05 17:18:56 -0700 (Thu, 05 May 2016) | 1 line
[Libra] Fix parameter handling (and avoid seg faults when a file is not found); changed progress bar style
r7284 | real_procopio | 2016-05-05 19:06:47 -0700 (Thu, 05 May 2016) | 1 line
[Petunia] Spruce up command status -- add border and shadow similar to other elements
r7285 | dshteyn | 2016-05-06 11:12:36 -0700 (Fri, 06 May 2016) | 1 line
PTMProphet: Don't use shared intensity to evaluate the mod positions, use the site determining ions.
r7286 | dshteyn | 2016-05-06 11:15:41 -0700 (Fri, 06 May 2016) | 1 line
Disco: adjust default settings and usage
r7287 | real_procopio | 2016-05-06 15:51:07 -0700 (Fri, 06 May 2016) | 1 line
[Petunia] Remove old IPP help pages; Moved Decoy Utilities in main menu to conserve space; added shadow to top of footer
r7288 | dshteyn | 2016-05-06 16:39:06 -0700 (Fri, 06 May 2016) | 1 line
PTMProphet: test that the modString is not a path , don't treat windows paths as a mod string.
r7289 | real_procopio | 2016-05-10 11:08:55 -0700 (Tue, 10 May 2016) | 1 line
[PepXMLViewer] Use the same color for any given PTM mod across all spectra (in page) -- implemented via a map/hash
r7290 | real_procopio | 2016-05-11 19:54:30 -0700 (Wed, 11 May 2016) | 7 lines
[ProtXMLViewer] - Fixed horizontal scrolling of column header (also added shadow effect to separate from main content) - Added ability to show/hide peptides for each protein - Changed color scheme and submit buttons to match new Petunia - Styled certain links so that they are more obvious targets to the user - Anchored footer to bottom of page, and styled it
r7291 | real_procopio | 2016-05-13 12:51:20 -0700 (Fri, 13 May 2016) | 9 lines
[ProtXMLViewer] - Enabled sorting by protein name/accession - Make page footer neatly stay in place at bottom of page, like all nice footers should - Highlight selected checkbox and radio options - Added spacer to fix bug that cropped rightmost column header on wide pages - Fixed wrapping of peptide page and menu bar on narrow displays - Fixed FireFox bug when displaying file stats: double border, background color was cropped - CSS tweaks...
r7292 | real_procopio | 2016-05-13 14:52:39 -0700 (Fri, 13 May 2016) | 1 line
[Marimba] REMOVE IT!
r7293 | real_procopio | 2016-05-13 15:44:29 -0700 (Fri, 13 May 2016) | 1 line
[Petunia] Restore call to FindBin; Always zip files when Downloading (even a single file)
r7294 | real_procopio | 2016-05-18 17:34:23 -0700 (Wed, 18 May 2016) | 10 lines
[Petunia] - Added ability to merge info from another session to current one
- Preserve login datetime, but override values otherwise, including working dir - Session can be selected from account drop-down, or linked from a file
- Added page for fetching datasets from public repositories (not linked yet!)
- Includes AJAX call to get system-specific capabilities for executable
- Added auto-filter for displaying jobs belonging to a specific session - Refactored a few session variables - Make filter box re-filter on blur - Re-saved config file with Linux line endings
r7295 | dshteyn | 2016-05-23 14:26:00 -0700 (Mon, 23 May 2016) | 1 line
DiscoFilter: build and install to bin not cgi-bin.
r7296 | dshteyn | 2016-05-23 15:46:26 -0700 (Mon, 23 May 2016) | 1 line
DiscoFilter: default settings to use internal HardKlor API
r7297 | dshteyn | 2016-05-24 09:51:13 -0700 (Tue, 24 May 2016) | 1 line
Disco: build target should point to BUILD_BIN instead of BUILD_CGI
r7298 | dshteyn | 2016-05-24 09:59:13 -0700 (Tue, 24 May 2016) | 1 line
Initialize fpkm count
r7299 | real_procopio | 2016-05-24 20:45:45 -0700 (Tue, 24 May 2016) | 5 lines
[Petunia] - Added (empty) directory delete functionality - Fixed file types for decoy peptide and protein analysis - Moved realpath use directive (to see if that will avoid the namespace collision with FindBin::libs)
r7300 | eng_jk | 2016-05-25 11:50:20 -0700 (Wed, 25 May 2016) | 2 lines
add array out of bounds check
r7301 | real_procopio | 2016-05-25 20:09:41 -0700 (Wed, 25 May 2016) | 8 lines
[Petunia] - Pass advanced/extra user options to Disco - Implemented max files limit on file chooser; give warning when over limit -- Updated pages that require this limit - Renamed 'ref_page' parameter to addFiles to more precise 'proctype' - Expanded max size for extra user options in all relevant tools - Call new(?) --showAbilitiesHTML to display fetchDataset info
r7302 | real_procopio | 2016-05-26 16:36:41 -0700 (Thu, 26 May 2016) | 1 line
[Petunia] Updated to more user-friendly tag names for session files (proc_types)
r7303 | real_procopio | 2016-05-31 19:25:28 -0700 (Tue, 31 May 2016) | 8 lines
[ASAPRatio] Boost performance by doing a single pass read of all peptides in source pepXML files (as opposed to reading all files for each protein!) Benchmarked speed-up at 200+ times over previous version - New psm struct to hold peptide data in a global vector; used to calculate protein ratios after all source files have been read into memory - Somehow fixed memory leak bug that caused some incorrect peptide assignments during ratio calculation - Record ASAPRatio version in protXML - Provide more feedback when running command (software name, version, and file being analyzed) as well as progress bar - Minor code reformatting and clean-up
r7304 | real_procopio | 2016-06-01 15:05:12 -0700 (Wed, 01 Jun 2016) | 7 lines
[ASAPRatio] Could not leave fast enough alone :: boosted performance by another factor of 2. This is now about ~400x faster than previous version. - Store peptide info in a map for faster lookup - Removed unnecessary Bool get_all_peptides from overloaded class signature - Also removed useless Next_Peptide and Previous_Peptide buttons from peptide curation interface - Some code formatting and clean-up
r7305 | real_procopio | 2016-06-01 18:20:03 -0700 (Wed, 01 Jun 2016) | 1 line
[Petunia] Remove FindBin::libs as it breaks the core Cwd perl module we use; fix xinteract output directory bug
r7306 | real_procopio | 2016-06-02 17:23:05 -0700 (Thu, 02 Jun 2016) | 7 lines
[ASAPRatio] - BUGFIX: do NOT write heavy2light_adj_ratio_standard_dev attribute unless it is a normalized value!! - BUGFIX: Increase tmp buffer size to 50k for javascript within interface to accomodate peptides with many identifications - Remove useless Prev_ and Next_Protein buttons from interface - Some code formatting and clean-up (this codebase needs a thorough bleaching and scrubbing...)
r7307 | mhoopmann | 2016-06-15 16:02:06 -0700 (Wed, 15 Jun 2016) | 2 lines
ProtXML parsing now understands that the probability table has been reversed. Improved warnings and error handling when data file paths have been broken in the XMLs.
r7308 | real_procopio | 2016-06-15 17:00:54 -0700 (Wed, 15 Jun 2016) | 1 line
[ProtXMLViewer] Add filter to exclude entries w/o Libra values; display 'inf' Libra values as 100%
r7309 | real_procopio | 2016-06-17 12:20:37 -0700 (Fri, 17 Jun 2016) | 1 line
[ProtProphetModels] Make sure we insert the <analysis_summary> tag set before <dataset_derivation> as per the schema. If none is present, fall back to first instance of <protein_group>
r7310 | real_procopio | 2016-06-17 13:41:39 -0700 (Fri, 17 Jun 2016) | 8 lines
[Libra] - Boosted performance by another factor of 20. This is now about ~500x-2000x faster than 4.8.0. -- Store peptide info in a map for faster lookup - Removed unnecessary Bool get_all_peptides from overloaded class signature - For not-a-number and infinity results, output XML_compliant "NaN" and "INF" values - Improved user feedback
r7311 | real_procopio | 2016-06-17 16:30:10 -0700 (Fri, 17 Jun 2016) | 1 line
[StPeter] Add schema-required attributes time and id to analysis_summary tag. Also save with Linux line endings instead of DOS...
r7312 | real_procopio | 2016-06-17 17:07:32 -0700 (Fri, 17 Jun 2016) | 1 line
[protXML schema] Adding StPeter and decoy analysis results, and updating Libra channel info
r7313 | real_procopio | 2016-06-17 17:08:33 -0700 (Fri, 17 Jun 2016) | 1 line
[protXML schema] Update to latest version of schema
r7314 | mhoopmann | 2016-06-20 14:02:24 -0700 (Mon, 20 Jun 2016) | 3 lines
Fixed redundancy in peptides listed for each protein (did not affect results). Made a few function call changes to silence valgrind warnings; StPeter functionality remains the same.
r7315 | mhoopmann | 2016-06-20 15:27:29 -0700 (Mon, 20 Jun 2016) | 3 lines
Changed timestamp format string to support compilers still using older standards (ahem...Microsoft...)
r7316 | dshteyn | 2016-06-24 16:46:10 -0700 (Fri, 24 Jun 2016) | 1 line
PTMProphet: Poisson and EM -- InteractParser, RefreshParser, PeptideProphet, iProphet, ProteinProphet: Kojak Support -- RTCatalog: tweaks to defaults -- Various other small tweaks.
r7317 | dshteyn | 2016-06-24 16:51:58 -0700 (Fri, 24 Jun 2016) | 1 line
Fix ambiguous reference
r7318 | dshteyn | 2016-06-24 17:08:29 -0700 (Fri, 24 Jun 2016) | 1 line
More ambiguous refs.
r7319 | dshteyn | 2016-06-24 17:39:10 -0700 (Fri, 24 Jun 2016) | 1 line
Remove unneeded
r7320 | mhoopmann | 2016-06-29 12:43:54 -0700 (Wed, 29 Jun 2016) | 4 lines
Swapped in sort() for qsort() to fix crashes in GCC 5.x.x Note: other instances of qsort() in the code appear to function correctly. Just this one has issues, and only with GCC 5 (4.x.x works fine).
r7321 | mhoopmann | 2016-06-29 13:00:40 -0700 (Wed, 29 Jun 2016) | 2 lines
fixed an output string to quiet warnings in GCC 5.3.1
r7322 | mhoopmann | 2016-06-29 13:02:35 -0700 (Wed, 29 Jun 2016) | 2 lines
updated version number and date
r7323 | dshteyn | 2016-07-06 11:50:35 -0700 (Wed, 06 Jul 2016) | 1 line
compareProts.pl: fix bug with JS_HOME.
r7324 | dshteyn | 2016-07-06 14:53:46 -0700 (Wed, 06 Jul 2016) | 1 line
compareProts_ClusterHM.pl: fix D3 and JS references.
r7330 | dshteyn | 2016-07-15 12:39:50 -0700 (Fri, 15 Jul 2016) | 1 line
RespectParser: BUGFIX: peptide string was not being cleared out properly.
r7331 | mhoopmann | 2016-07-18 14:47:51 -0700 (Mon, 18 Jul 2016) | 3 lines
Fixed bug in which peptides read from prot.xml files without iprophet were being ignored.
r7333 | real_procopio | 2016-07-26 13:21:21 -0700 (Tue, 26 Jul 2016) | 1 line
[Tandem2XML] Remove non-schema compliant search_engine attribute from msms_run_summary tag
r7334 | real_procopio | 2016-07-27 14:24:23 -0700 (Wed, 27 Jul 2016) | 11 lines
[pepXML schema] First pass at updating pepXML schema; minor extra work is needed to add new desired features
- Added support for cross-linking results - Added (belated) support for PTMProphet results - Modified unique_search_summary_basename restriction to also include search_engine -- this allows for combining of multiple search engine results of the same source files (e.g. iProphet) - Created new data type declarations for reusable elements alternative_protein and modification_info - Removed errant search_engine attribute from msms_run_summary (was mistakenly re-added in v118) - Added YABSE, MS-GF+, and Kojak to list of known search engines
r7335 | real_procopio | 2016-07-27 14:50:36 -0700 (Wed, 27 Jul 2016) | 1 line
[pepXML schema] Bump to v120
r7336 | dshteyn | 2016-07-29 08:15:18 -0700 (Fri, 29 Jul 2016) | 1 line
BUGFIX: Null the pointers after deleting to prevent deleting twice, which breaks with gcc.
r7337 | real_procopio | 2016-08-03 14:13:24 -0700 (Wed, 03 Aug 2016) | 7 lines
[pepXML schema] Clean up support for PTMProphet results - Enable multiple tags within <analysis_result> - Added ptmprophet_summary declaration Added initial support for SAAV results in anticipation of full PEFF support Minor Interprophet typo correction
r7338 | dshteyn | 2016-08-03 15:06:26 -0700 (Wed, 03 Aug 2016) | 1 line
PTMProphet: fix pepxml reporting to conform to schema. New EM models.
r7339 | real_procopio | 2016-08-04 14:56:45 -0700 (Thu, 04 Aug 2016) | 7 lines
[Petunia] - Fix reference to ProteoGrapher - Show all TPP tools under Kojak pipeline - Switch SWATH -> DIA - Add \n to properly display message when user forces a command to terminate - Keep [?] help link next to parameter (do not line break)
r7340 | real_procopio | 2016-08-04 15:02:14 -0700 (Thu, 04 Aug 2016) | 5 lines
[ProtXMLViewer] - Export stpeter value to Proteographer, if present - Always test for 'INF' in Libra ratios by forcing uppercase on value - Removed unneeded File::Copy include
r7341 | real_procopio | 2016-08-04 17:40:03 -0700 (Thu, 04 Aug 2016) | 1 line
[kojak] Adding Kojak to TPP. To keep it simple, we just check in the binaries downloaded from kojak-ms.org. Also installs conf (parameters) file.
r7342 | real_procopio | 2016-08-04 17:41:48 -0700 (Thu, 04 Aug 2016) | 1 line
[kojak] Adding Kojak to TPP. To keep it simple, we just check in the binaries downloaded from kojak-ms.org. Also installs conf (parameters) file.
r7343 | real_procopio | 2016-08-04 17:43:29 -0700 (Thu, 04 Aug 2016) | 1 line
[comet] Latest version of comet -- 2016012
r7344 | real_procopio | 2016-08-04 17:47:34 -0700 (Thu, 04 Aug 2016) | 1 line
[PepXMLViewer] Display linked position of XL peptides
r7345 | real_procopio | 2016-08-04 17:53:56 -0700 (Thu, 04 Aug 2016) | 1 line
[TPP 5.0.0] Behold our first RC of Omega Block!
r7346 | dshteyn | 2016-08-09 11:07:49 -0700 (Tue, 09 Aug 2016) | 1 line
PTMProphet: memory delete bug fix.
r7347 | dshteyn | 2016-08-09 11:10:05 -0700 (Tue, 09 Aug 2016) | 1 line
RespectParser: BUFIX sort the output by scan number and reindex in order of scan number for iProphet multipe search engine results to be properly encoded.
r7348 | real_procopio | 2016-08-09 19:21:48 -0700 (Tue, 09 Aug 2016) | 1 line
[xtandem] Do not remove trailing path designator
r7349 | real_procopio | 2016-08-09 19:25:36 -0700 (Tue, 09 Aug 2016) | 1 line
[params] Make sure params are under www access and with rw permissions; Properly configure tandem_params.xml; Fix svn ID in code
r7350 | real_procopio | 2016-08-09 19:31:42 -0700 (Tue, 09 Aug 2016) | 1 line
[Petunia] Add warning if Percolator is not installed; Update to new MZTOL default for reSpect; add var declaration to javascript variable
r7351 | real_procopio | 2016-08-09 20:07:12 -0700 (Tue, 09 Aug 2016) | 1 line
rc2
r7352 | real_procopio | 2016-08-10 11:28:56 -0700 (Wed, 10 Aug 2016) | 1 line
[pepXML schema] Adding optional "source" attribute for modification site info
r7353 | dshteyn | 2016-08-10 14:44:09 -0700 (Wed, 10 Aug 2016) | 1 line
Remove debug message
r7354 | dshteyn | 2016-08-10 15:21:10 -0700 (Wed, 10 Aug 2016) | 1 line
Remove debug message
r7355 | real_procopio | 2016-08-10 19:04:33 -0700 (Wed, 10 Aug 2016) | 1 line
[make] Remove errant comment that caused build to crash
r7356 | real_procopio | 2016-08-11 16:57:37 -0700 (Thu, 11 Aug 2016) | 1 line
[Windows installer] Is this where the string replacement is supposed to happen...?
r7357 | real_procopio | 2016-08-12 17:20:53 -0700 (Fri, 12 Aug 2016) | 1 line
[TagFilter] Undo change that broke PvalueParser (and potentially other TPP components
r7358 | real_procopio | 2016-08-12 17:29:17 -0700 (Fri, 12 Aug 2016) | 1 line
[ASAPpvalue] Do not crash if model file is not under webserver_root - just give a warning; Do not attempt to open a file if none is given in input parameters (duh...)
r7359 | real_procopio | 2016-08-12 17:29:57 -0700 (Fri, 12 Aug 2016) | 1 line
RC3
r7360 | real_procopio | 2016-08-16 18:08:30 -0700 (Tue, 16 Aug 2016) | 1 line
[constants] Remove duplicated define
r7361 | real_procopio | 2016-08-16 18:12:19 -0700 (Tue, 16 Aug 2016) | 1 line
[XPress] Get location of xsltproc via getBinPath call in non-Linux systems (removing hard-coded reference to old C:\Inetpub\tpp-bin\). Minor code clean-up
r7362 | real_procopio | 2016-08-16 18:13:58 -0700 (Tue, 16 Aug 2016) | 1 line
RC4
r7363 | real_procopio | 2016-08-17 14:00:03 -0700 (Wed, 17 Aug 2016) | 1 line
[util] Synchronize Jimmy's commits 7083 and 7084 from trunk. Update README
r7364 | real_procopio | 2016-08-17 14:29:34 -0700 (Wed, 17 Aug 2016) | 1 line
[XPress] Synchronize Jimmy's commits 7101 and 7102 from trunk. Also added svn Id tag and removed redundant util.h include
r7365 | real_procopio | 2016-08-17 14:43:14 -0700 (Wed, 17 Aug 2016) | 1 line
[subsetdb] Synchronize Jimmy's commits 7195, 7198, 7261, 7269, and 7332 from trunk. Also added svn Id tag
r7366 | real_procopio | 2016-08-17 15:40:32 -0700 (Wed, 17 Aug 2016) | 1 line
RC5
r7367 | real_procopio | 2016-08-17 19:08:01 -0700 (Wed, 17 Aug 2016) | 4 lines
[ProtXMLViewer] - Added links to PeptideAtlas and Protter - Format reported XPress weighted global ratio and percent psm's used therein
r7368 | real_procopio | 2016-08-18 16:57:47 -0700 (Thu, 18 Aug 2016) | 1 line
[kojak] Update to 1.5.1 (fixes multi-thread bugs). Also make sure it is called Kojak.exe in Windows!
r7369 | dshteyn | 2016-08-18 22:51:56 -0700 (Thu, 18 Aug 2016) | 1 line
InteractParser: populate sample_enzyme tag when not present, this tag is required for RefreshParser.
r7370 | dshteyn | 2016-08-18 22:55:12 -0700 (Thu, 18 Aug 2016) | 1 line
KojakResult: store the higher scoring peptide score in another member.
r7371 | dshteyn | 2016-08-18 23:02:22 -0700 (Thu, 18 Aug 2016) | 1 line
PeptideProphetParser: Kojak Support. InterProphetParser: minor. DiscoFilter: Now works when the first scan is not MS1, and will not crash passing the last scan.
r7372 | dshteyn | 2016-08-18 23:04:29 -0700 (Thu, 18 Aug 2016) | 1 line
PeptideProphet: new model for Kojak XL.
r7373 | dshteyn | 2016-08-19 08:08:09 -0700 (Fri, 19 Aug 2016) | 1 line
xl option
r7374 | dshteyn | 2016-08-19 08:38:28 -0700 (Fri, 19 Aug 2016) | 1 line
XLSecondScoreFractionMixtureDistr Model compilation.
r7375 | dshteyn | 2016-08-21 16:29:46 -0700 (Sun, 21 Aug 2016) | 1 line
InteractParser: don't filter out InteractParser tags, they show a record of the corrections applied to the pepXML file...also fix a bug with unclosed analysis_summary tags...
r7376 | real_procopio | 2016-08-22 17:40:19 -0700 (Mon, 22 Aug 2016) | 1 line
[Windows installer] Ensure forward slashes for INSTALL_PARAMS path
r7377 | mhoopmann | 2016-08-24 09:02:43 -0700 (Wed, 24 Aug 2016) | 2 lines
Added parameter to convert SIn to ng.
r7378 | real_procopio | 2016-08-24 15:47:31 -0700 (Wed, 24 Aug 2016) | 1 line
[Windows installer] Place params files within the actual desired directory, and not the incorrectly used 'users/' dir
r7379 | real_procopio | 2016-08-24 16:42:20 -0700 (Wed, 24 Aug 2016) | 1 line
[Petunia] Preset a few xinteract defaults for Kojak-based analysis
r7380 | real_procopio | 2016-08-24 16:45:07 -0700 (Wed, 24 Aug 2016) | 1 line
[kojak] Set default threads value in sample conf file to something more common
r7381 | real_procopio | 2016-08-24 17:02:37 -0700 (Wed, 24 Aug 2016) | 1 line
RC6
r7382 | real_procopio | 2016-08-25 13:13:19 -0700 (Thu, 25 Aug 2016) | 1 line
[pwiz msi] Updating to latest...hope it works
r7383 | real_procopio | 2016-08-25 16:23:47 -0700 (Thu, 25 Aug 2016) | 1 line
RC7 - new Win-PWIZ
r7384 | real_procopio | 2016-08-26 11:55:38 -0700 (Fri, 26 Aug 2016) | 1 line
[filtertable] Added convenience function to allow quick-filtering of tables; also force filter when filter box is blank
r7385 | real_procopio | 2016-08-26 12:16:31 -0700 (Fri, 26 Aug 2016) | 8 lines
[Petunia] - Do not show directories when looking for files - Added quick links to view jobs by status (including 'ALL') - Fix formatting of message when no jobs are present - Switch to using new set_filter js function for filtering list via link - Add links to open pdf and jpg files - Added two extra simple link styles
r7386 | real_procopio | 2016-08-26 12:47:21 -0700 (Fri, 26 Aug 2016) | 1 line
[Petunia] Link directly to MODELS file when running either of the ProphetModels decoy validation tools
r7387 | dshteyn | 2016-08-29 12:16:33 -0700 (Mon, 29 Aug 2016) | 1 line
tpp_gui.pl: DiscoFilter - BATCH is no longer necessary
r7388 | dshteyn | 2016-08-29 12:17:56 -0700 (Mon, 29 Aug 2016) | 1 line
version bump
r7389 | dshteyn | 2016-08-29 13:12:41 -0700 (Mon, 29 Aug 2016) | 1 line
PTMProphet: REMOVE modstring from the model name so not to break parsing by the _MODELS.html page.
r7390 | real_procopio | 2016-08-29 14:39:42 -0700 (Mon, 29 Aug 2016) | 1 line
[protXML viewer] Ensure forward slashes in file paths; always link to Protter in new tab/window
