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FragPipe v12.0
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@chhh chhh released this 09 Nov 20:57
· 3566 commits to master since this release
12.0
80ac789

FragPipe v12.0

Windows users

  • Download FragPipe.exe 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.
  • Or download FragPipe-12.0.zip.
    • Zip contains FragPipe.bat file, which can be started by either clicking or running it from the command line.
  • Or download the FragPipe-12.0.jar.
    • You can start the jar file with java -jar FragPipe-12.0.jar or start javaw -jar FragPipe-12.0.jar if you prefer to not have the console window open.
      If Java is configured to auto-run .jar files, double clicking might also work.

Linux/MacOS users

  • Either download FragPipe-12.0.zip, which contains FragPipe shell script to start the program
  • Or download the FragPipe-12.0.jar and run with java -jar FragPipe-12.0.jar.

Changelog:

v12.0:

  • Add IMQuant - quantitation for timsTOF.
  • PTMShepherd updates - in-depth PTM analysis and reporting.
  • Fix running FragPipe without an internet connection.
  • Choice of default enzyme specifications in MSFragger config.

v11.0:

  • Parallel execution engine. Used only for PeptideProphet now, utilizing all CPU cores.
  • DIA-Umpire requires MSConvert from ProteoWizard on Linux.

v10.0:

  • Add PTMShepherd with UI.
  • Thermo RAW files and Bruker TimsTOF .d directories are supported. They do require new MSFragger with 'ext' directory for libraries and additional binaries.
  • Fix for changes to modification tables not always being propagated to config files if the user didn't leave the editing field.
  • Saving all the FragPipe options before run + buttons to Save/Load configurations.
  • Fix iProphet command threads and how it's invoked when multi-experiment is enabled.
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