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FragPipe v9.4
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@chhh chhh released this 30 May 23:57
· 563 commits to gh-pages since this release
9.4
9780638

Windows users

  • Download .exe: 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 .zip: FragPipe-9.4.zip.
    • Zip contains FragPipe.bat file, which can be started by either clicking or running it from the command line.
  • Or download the FragPipe-9.4.jar.
    • You can start the jar file with java -jar FragPipe-9.4.jar or start javaw -jar FragPipe-9.4.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-9.4.zip, which contains FragPipe shell script to start the program or download the FragPipe-9.4.jar and run with java -jar FragPipe-9.4.jar.

FragPipe v9.4 changelog:

v9.4:

  • Fixes to MSFragger Split program for very large databases.

v9.3:

  • Calibrate masses option in MSFragger
  • Custom ion series option in MSFragger
  • Turning off usage of protxml file in Filter command when Protein Prophet is not run
  • Query user if protxml files exist while Protein Prophet is not run
  • 'Print Decoys' option/checkbox for Report command
  • Update CrystalC-1.0.5
  • Checkbox for generating report in mzID format
  • UI for downloading protein databases via philosopher

v9.1:

  • Fix Abacus command bug with unrecognized options from Filter command being carried over.

v9.0:

  • Downstream tab groups all downstream processing tools in one place.
  • Simplified Config tab with more links and hint.
  • Much improved saving and restoring of edited fields.
  • Support MSFragger 20190222
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