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FragPipe v7.1 (previously MSFragger-GUI. Includes MSFragger, Peptide/Protein Prophets, Philosopher Reports
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@chhh chhh released this 21 Jul 02:01
· 4507 commits to develop since this release
v7.1
5babcff

Windows users

  • You may download the .zip file.
    • You can start the jar file with start javaw -jar FragPipe.jar or java -jar FragPipe.jar or using the provided .bat script in the zip archive. If Java is configured to auto-run .jar files, double clicking might also work.
  • You may download the .exe file and just run that. Windows 10 might show a UAC prompt, saying that this is not a trusted program, it's up to you whether to run it or not.
    • If you don't have a compatible Java version, you will be redirected to a website where you can download one.

Linux/MacOS users

Download the .zip file and either run the included launcher shell script or just with java -jar FragPipe.jar.

FragPipe v7.1 changelog:

v7.1:

  • Added label free quantitation.

v7.0:

  • MFFragger-GUI is now calledFragPipe.
  • Clear out Fragger modification tables when loading new parameter files to avoid ghost entries.
  • Update the github urls for checking new versions.

v6.0.1:

  • Allow loading of empty-valued parameters from fragger *.properties files.
  • Comments in fragger.properties won't overwrite non-commented properties anymore.

v6.0:

  • Automatic updates for MSFragger
  • mass_offsets parameter for MSFragger
  • Lower default number of fragments required in Closed search to 4
  • Improved tooltips in MSFragger tab
  • Initial defaults are loaded for Closed search now instead of Open

v5.4:

  • Restore last location of MSfragger params file save/load operation.
  • Show errors from loading msfragger.params files

v5.3:

  • Button for auto-detection of decoy prefixes
  • When sequence DB changes, display the number of proteins.
  • Auto-detect buggy cached --clevel option and change it to -2.

v5.2:

  • Revert PeptideProphet --clevel option default to '-2' for Open Searching.

v5.1:

  • Bug fixes for cross-tool decoy tag updates.

v5.0:

  • Separate tab for sequence database.
  • Display info about known compatibility of newer versions of Philosopher.

v4.9:

  • Stop execution of the pipeline if one of the processes returns non-zero exit code.
  • Colorize console output a bit, red color for errors.
  • Button that redirects to the issue tracker online for bug reporting.

v4.8:

  • Introduce notifications about update contents
  • User-message can now be shown without a newer version available
  • Added export button and context menu item to the console to simplify bug reporting by users.

v4.7:

  • Support new packaging of MSFragger jar with onejar.

v4.6:

  • Fix mixed up order of philosopher calls.

v4.5:

  • Show parsed versions of tools in the UI.
  • Print detected versions of tools to console before each run.

v4.4:

  • Only run Philosopher workspace --clean/--init once per analysis.

v4.3:

  • Locale dependency fix for MSfragger parameters panel.
  • Philosopher checks version comparing to GitHub at startup.

v4.2:

  • Fix the issue that Fragger panel constructor could cause IOException and prevent the whole app from loading.

v4.1:

  • Variable mod site definition warning text if cached from older versions.
  • Java 9 warning for Fragger.
  • Non-symmetric precursor mass tolerance and detection of "[*" for var mods.
  • Cache fragger params after a dry-run or a real run.

v4.0:

  • Added version check for MSFragger-GUI itself, comparing to GitHub.
  • Two way sync of decoy/tag prefix used by Peptide Prophet and Philosopher Report.
  • Fix how msfragger jar is auto-found.
  • Added version to msfragger properties.
  • MSFragger version check.
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