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ReleasePreparation

Dave Brondsema

this page collects dates and tasks for the upcoming release

Release 1.8

Dates

  • Feature-Freeze: 03.02.2011
  • Branch: 04.02.2011 (Chris)
  • Release: 06.03.2011

Tasks

General

Testing

  • Simulator
  • Id-View
  • TOPPAS in TOPPView
  • external tool support
  • alignment-trafo Entkopplun

Release 1.7

Dates

  • Feature Freeze: 01.08.2010
  • Release branching: 04.08.2010 (only branch when CDash is clean? since Monday its a mess)
  • Release candidate: 15.08.2010
  • Testing, package building: 15.08.2010 - 31.08.2010
  • Release of (source+binaries): 31.08.2010

Tasks

  • coordinator in TĂźbingen: Mathias
  • review TOPP docu (Mathias assigns each developer some tools; ideas on what is missing can be collected here)
  • test installers on multiple machines/setups. Check all tests, but also the tools, including working thrhough the tutorials
  • TOPPAS tutorial (Hannes?)
  • TOPPAS workflow collection (bring them to the Retreat, we'll upload them on openms.de afterwards)
  • Each example workflow should also come with 1-3 example data sets -- real life datasets obtained from our exptl. collaborators [example pipelines/data from Dortmund workshop, Lars]
  • Make sure database search engines are included in the binary (Win/Mac) distributions so people can use them out of the box.
    • Are we even allowed to do that? (license?)
    • this is only of limited usage for OMSSA, as the user needs to format the DB with BLAST beforehand.
    • Can we also find a solution for package-based installation under Linux (are there linux packages for X!T, OMSSA?)

  • What is the status of the generic TOPP tool?

    • GenericWrapper?? Works just nicely. Currently used for wrapping Proteowizard's msconvert.
    • We should either
    • add specialized versions of GenericWrapper? to the list of TOPP tools in TOPPAS (extendable via a config file)
      • advantage: we distribute new wrappers to users, just by sending a config file
    • type GenericWrapper? (-type msconvert, -type ..., -type user_defined)
      • advantage: also usable in non-TOPPAS workflows, but new types require a new OpenMS

  • revise TOPP (optional withdrawal: sequest/inspect adapters; optional replacement crux??)

  • remove/hide entire tools [ ]#171 Chris
  • remove/hide deprecated algorithms (such as in FeatureFinder?, FeatureLinker?, ConsensusID, ...) [ ]#152 Hendrik
    • candidates (Developer vote):
    • FeatureFinder?:
      • "simple" (name)
      • "simplest" (name)
    • FeatureLinker?:
      • "identification" (name)
    • no candidates:
    • vote will be merged into ticket [ ]#152 Hendrik at 10. August
  • rework TOPPView data management [ ]#100 Timo
  • see http://sourceforge.net/apps/trac/open-ms/wiki/UpcomingRelease

TOPP tool docu revision

  • what should be contained in every TOPP/UTIL tool:
    • possible Predecessor and Successor tools (e.g. FeatureFinder? should say: PeakPicker? before (for centroided FF) and MapAligner?, IDMapper after)
    • ...
  • look at parameter documentation.
    • is the description explanatory or does it just rephrase the parameter name (NOT HELPFUL!)
    • is the name appropriate? Should the name be in a subcategory (useful for specific sub-settings, e.g. <category>:<param>, see IDFilter as an example)
  • Provide docu in the tutorial about saving and executing pipelines from the command line
  • Provide limited assistence for identification-engine install (i.e. link out to OMSSA and X!Tandem)

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