ReleasePlanning
From SPCTools
This page is intended to assist in release planning by tracking new feature requests/bugs/improvements etc for TPP.
Contents |
For Next Release
Planned timeline
- Release 4.7.0
Completed Tasks
- IMPROVEMENT: We need to update pepXML Viewer to display the search scores from Myrimatch.
- (Luis) NEW FEATURE: Include viewer support for msgfplus
- (Joe&Mike) IMPROVEMENT: Upgrade X!Tandem
- Petunia now looks for any *params* file and recognizes Tandem-specific ones; also added basic editing page
- (Luis) IMPROVEMENT: Add support for XPRESS ppm tolerance (-a) to Petunia
- (Luis) BUG: Use of qw in tpp_models.pl posted on spctools
- (Luis) Remove Petunia interface to PepC. It has rotted. But leave code in repository.
- (Joe) IMPROVEMENT: Updated boost to 1.54
- (Joe) IMPROVEMENT: Incorporated updated MacOS X support/clang 5.0 generously provided by David Trudgian
- (David) BUG: Using deprecated option -MONO in the xinteract command throws an exception spctools
- (David) BUG: InteractParser issue in 4.6.2 reported by Jimmy on spctools. Something about the last spectrum_query in the pepXML file containing no search results. (fixed by David Trudgian, merged by Joe Slagel)
- (David) BUG/IMPROVEMENT: update usage in InteractParser to include *all* of the parameters it recognizes. Should also probably exit with a non-zero status and message when a parameter that it doesn't recognize is given.
- (David) BUG: exception being thrown by PeptideProphetParser instead of printing usage when invoked without any arguments
- (Joe) NEW FEATURE: updateAllPathsNoReallyThisTime.pl
- (Luis) NEW FEATURE: Support of Comet in Petunia, prophets, quant, viewers
- (Luis) Removed 'Confidence' metric from ProteinProphet.
- (Joe) Update bundled Apache version in Windows distro
- (Joe) IMPROVEMENT/BUG: Don't report an invalid amino acid character in X!Tandem if its a '*' character
- (Luis) BUG: TPP_Demo2009 db dataset has a parameters file named tandem.xml. It needs to be named tandem.params now.
- (Luis+Joe) NEW FEATURE: Petunia can now run commands on SGE using qrsh.
- (Luis+Joe) NEW FEATURE: Petunia can now run commands as authenticated user using sudo command.
- (Joe) BUG: Fix next round of Viva64 bugs reported on the mailing list
- (Joe) NEW FEATURE: Bundle Mayu in TPP installer
- (Joe) TODO: updatepaths may not always handle paths correctly when being run on files from other operating systems, e.g. updating the paths of a file copied from a Win32 system to a Linux system. Has to do with File::Spec::splitpath not splitting Win32 paths at all since we're on a linux system. Consider trying File::Spec::Win32 first regardless of platform.
- (Joe&David) Issues with mingw versions, gcc versions, and -lpthread vs -lpthread-dll
- (Joe&Luis) NEW FEATURE: Add a Mayu interface in Petunia
- (Joe) IMPROVEMENT: Update Pwiz on the Linux side! Wait until Matt is done upgrading Boost, and then yes!
Pending Tasks
- Build RC and test
DEFERRED
- (Joe) TODO: Include documentation on how to configure sudo/SGE for petunia
- (Eric+Joe+Steve) NEW FEATURE: Bundle idConvert, Petunia page, Steven is fixing it and working with Matt
- (Joe) NEW FEATURE: Add ability to include CPAN modules in TPP installer for AMZTPP
- (Joe) IMPROVEMENT: Include amztpp in the distribution
- (Joe) IMPROVEMENT/BUG: Have the TPP installer fill in the correct paths in tpp_gui.pl when building. Warn if a program can't be found. On Windows it seems to have a hardcoded path to perl so that the programs/cgi scripts fail if you put perl in another location, e.g. installing 64 bit perl which goes to C:\Perl64 instead of C:\Perl. Recently tried the 64 bit version and found that the installer throws ugly perl errors in the installation. The cgi scripts however seem to work.
- (Luis) NEW FEATURE: Support of OMSSA and hrk-score in the Petunia, prophets, quant, viewers
- (Joe+Luis) Create a centralized path furnishing system
- (Luis/Joe) BUG: lorikeet uses hardcoded paths to the html and javascript directories on the Apache server (e.g. ISB/js/lorikeet.js) instead of using the TPP_WEB Makefile variable.
- (David) BUG: Problem correcting mzXML file paths in 4.6.2 reported on spctools, Submitted by John Chilton, but a repro was never sent, Couldn't be reproduced on own data.
- (Luis) NEW FEATURE: Provide a db fmt/verifier that gets run as an optional first step in petunia
- (Joe) BUG: new decoy generator doesn't know about NCBI "|" so creates funny sequence ids
- Rewrite QualScore in portable C++ to retire Java
- Have a nightly Windows build
- Joe would love to rewrite the Make file
Miscellaneous Ideas
List of suggested TPP new features, improvements, fixes, etc.. to be cherry picked for upcoming releases.
- MzXML2Search is used to convert mzML files to mgf for searching with OMSSA. Do we even need this program with the
capabilities of msconvert? Only ask as I have a set of files its crashing on right now and it works for msconvert...
- Drop CompactParser. Doesn't seem to work.
- Breakout apache configuration into its own file and handle it properly on Ubuntu systems
- (Luis?) IMPROVEMENT: This one goes to "11", or in this case 10. Charge states above +9 will no doubt cause trouble in TPP.
- NEW FEATURE: PEFF support in TPP. (Need to define what this means).
- 64 bit version of TPP? mingw-64 is stable now. http://mingw-w64.sourceforge.net
- Better support for viewing/outputting N15 experiments. Sequences are hard to read (modification every base) and makes the xml huge.
- Add ASAPRatio option to use WaveletQuant in Petunia
- Verify that xinteract can deal with this option (-w)
- Petunia: option to run xinteract jobs as separate (instead of combining into a single analysis)
- Make sure new installation of QualScore works on Windows
- Output more significant figs for Protein Prophet weight (rounding error on 0.49 and 0.50)
- Fix precursor charge column (only 1st letter displayed) and miscalculation of the # of unique peptides in EXCELPEPS
- EXCELPEPS appears to be broken; just remove it?
- Resolve Andreas issue with Tandem2XML
- Write (TPP) software version used in pepXML, protXML, etc
- Silence/catch errors on the *Prophet models generation when no data (e.g. "empty y range")
- Zhi has been experiencing a bus error one large operation with SpectraST
- There is a was a reported bug by Henry with mzParser
- Add commandline option to generate EXCEL output of pepXML files
- Issue with MzXML2Search converting older mzXML files to mgf. Randomly fails on the same file.
- Missing javascript file for table filtering in Petunia (only affects Linux installations)
- I encountered a small problem when using the new TPP. In the prot.shtml view, pink color coding of NxS/T motifs does not work anymore when checking the box. Also, I always liked the "464 peptides with NXS/T motif, 690 total peptides, 658 unique stripped peptides"info at the bottom of the page (as it gives us an immediate idea of how nicely a glyco experiment worked) but this is not displayed correctly anymore.
- Included Terry's latest version of Inspect2PepXML.py for patching inspect installations
- Bug: Petunia will (re-)submit a new job if the "back" button is clicked after the initial job launch (Windows only)
Legacy Items
Fix iProphet models page ("performance" models are missing)
- Add "Bruker" files option to msconvert in Petunia
- Fix pepxml2html (View Peptide hits) peptide link for SpectraST results
- peptidexmlhtml2 : does not work with AA highlighting option (mark_aa=)
- Add some filtering options to Pep3D (specifically: view only +1 ions)
- Add QuickMod to speclibs page?
- retire getSpectrum -> use readMzXML
- incorporate psm2pdf
- include t2d support(?)
- Petunia: option to convert to mzXML using msconvert
- Petunia: launch all external links in blank/target window
- Reindex mzXML: new file with old name; rename old to: old-index or some such
- Petunia: option to run xinteract jobs as separate (instead of combining into a single analysis)
- Petunia: select pep.xml files only for input to Decoy Models pages
- Petunia: auto cd to dir and strip out full path if all files in same dir (shorten command line)
- Petunia: rename Mascot file on download
- Move /tmp/ directory under tpp-bin (Windows)
- Petunia: Add TPP version check (ping server) --> usage stats
- Petunia: add full filters to msconvert(??)
- Petunia: change tab graphic when jobs are done?
- PepXMLViewer: implement "preferences" tab: choose ions series, spectrum viewer, etc... ?
- PepXMLViewer: no pep-pro probability link in iProphet results
- Libra also needs some love (ability to curate ratios would be a great start...)
== From Henry (perhaps he already checked this in?) :
Following up on this discussion, I would like to propose the following. (This is not urgent since our course doesn't use OMSSA or any of the newly-supported engines, so it doesn't need to be in the release soon.)
1. Change xinteract to run RefreshParser before PeptideProphet.
This takes care of the protein name issues for OMSSA, and makes sure that the NTT and NMC fields are there and calculated correctly for PeptideProphet. Some search engines don't fill in those fields and cause PeptideProphet to crash.
The flip-side is mainly inefficiency. If the user decides not to keep all search hits regardless of probability (i.e. not specifying -p0), then this means RefreshParser unnecessarily refresh a bunch of wrong identifications that won't be in the final pepXML file anyway. But then again, given that nowadays PeptideProphet often relies on the protein name (whether it's a DECOY or not), it seems safer to ensure that the protein names are right -- even for the wrong hits -- before we run PeptideProphet. Also, with the new implementation, for most files RefreshParser is so fast that I don't think it will make much difference in running time anyway.
If the user doesn't want to refresh, he/she can always turn off RefreshParser (-nR option).
2. Have InteractParser detects if the search engine is OMSSA, and if so, apply the fix_pyro_mods_ option automatically.
This goes without saying. The only thing is the user doesn't have to turn on the option manually. I don't know if other engines have the same problem. If so, it's easy to add them to the list.
