ReleasePlanning

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Revision as of 20:40, 29 October 2013 Edeutsch (Talk | contribs) (→Planned timeline) ← Previous diff		Revision as of 20:42, 29 October 2013 Edeutsch (Talk | contribs) (→Completed Tasks) Next diff →
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	* IMPROVEMENT: We need to update pepXML Viewer to display the search scores from Myrimatch.		* IMPROVEMENT: We need to update pepXML Viewer to display the search scores from Myrimatch.
-	* (Luis) NEW FEATURE: Include support for msgfplus	+	* (Luis) NEW FEATURE: Include viewer support for msgfplus
	* (Joe&Mike) IMPROVEMENT: Upgrade X!Tandem		* (Joe&Mike) IMPROVEMENT: Upgrade X!Tandem
	* Petunia now looks for any *params* file and recognizes Tandem-specific ones; also added basic editing page		* Petunia now looks for any *params* file and recognizes Tandem-specific ones; also added basic editing page

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Revision as of 20:42, 29 October 2013

This page is intended to assist in release planning by tracking new feature requests/bugs/improvements etc for TPP.

Contents 1 For Next Release 1.1 Planned timeline 1.2 Completed Tasks 1.3 Pending Tasks 2 Miscellaneous Ideas 3 Legacy Items

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

Pending Tasks

• (Unassigned) BUG: Next round of via bugs reported on the mailing list

• (Luis) NEW FEATURE: Support of Comet in the prophets, quant, viewers

• (Luis) NEW FEATURE: Support of OMSSA in the prophets, quant, viewers

• (Joe) NEW FEATURE: updateAllPathsNoReallyThisTime.pl

• (Joe) NEW FEATURE: Add ability to include CPAN modules in TPP installer for AMZTPP

• (Eric+Joe+Steve) NEW FEATURE: Bundle idConvert, Petunia page, Steven is fixing it and working with Matt

• (Luis+Joe) NEW FEATURE: SGE job submission support (so that users can finally use 100% of petunia at ISB)

• (Luis) NEW FEATURE: Provide a db fmt/verifier that gets run as an optional first step in petunia

• (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.

• (Joe) IMPROVEMENT: Include amztpp in the distribution

• (Joe) IMPROVEMENT: Update Pwiz on the Linux side!

• (Joe) BUG: new decoy generator doesn't know about NCBI "|" so creates funny sequence ids

• (Joe) BUG: 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.

• (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.

• (Joe) IMPROVEMENT/BUG: Don't report an invalid amino acid character in X!Tandem if its a '*' character

• BUG: Using depreciated option -MONO in the xinteract command throws an exception spctools

• 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.

• BUG: Problem correcting mzXML file in 4.6.2 reported on spctools

• BUG: exception being thrown by PeptideProphetParser instead of printing usage when invoked without any arguments

• 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.

Miscellaneous Ideas

List of suggested TPP new features, improvements, fixes, etc.. to be cherry picked for upcoming releases.

• 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.

• Spectrast: https://groups.google.com/forum/#!topic/spctools-discuss/FuBFoPlTx80

• Confidence

So I saw again today Luis squirming under the question what is the “confidence” metric in ProteinProphet. It seems like it’s just confusing people. I suggest we sneak in a quick fix before the release of 4.6.3 to add an option to enable the printing of the confidence metric and that option be OFF by default. So that people who still want to use it can by setting an option, but by default most users will not be troubled by this.

• 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)
• Figure out installation of PepC (B.Pratt?)
• 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.