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@chhh chhh released this May 24, 2019 · 0 commits to gh-pages since this release

FragPipe v9.3

Windows users

  • Download .exe: FragPipe.exe and just run that. Windows 10 might show a UAC prompt, saying that this is no
    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-9.3.zip.
    • Zip contains FragPipe.bat file, which can be started by either clicking or running it from the command line.
  • Or download the FragPipe-9.3.jar.
    • You can start the jar file with java -jar FragPipe-9.3.jar or start javaw -jar FragPipe-9.3.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-9.3.zip, which contains FragPipe shell script to start the program or download
the FragPipe-9.3.jar and run with java -jar FragPipe-9.3.jar.

FragPipe v9.3 changelog:

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
Assets 5

@chhh chhh released this Feb 26, 2019 · 82 commits to develop since this release

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-9.1.zip.
    • Zip contains FragPipe.bat file, which can be started by either clicking or running it from the command line.
  • Or download the FragPipe-9.1.jar.
    • You can start the jar file with java -jar FragPipe-9.1.jar or start javaw -jar FragPipe-9.1.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-9.1.zip, which contains FragPipe shell script to start the program or download the FragPipe-9.1.jar and run with java -jar FragPipe-9.1.jar.

FragPipe v9.1 changelog:

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
Assets 5

Windows users

  • 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.
  • Or download the .jar file.
    • You can start the jar file with java -jar FragPipe-9.0.jar or start javaw -jar FragPipe-9.0.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

Download the .jar file and run with java -jar FragPipe-9.0.jar.

FragPipe v9.0 changelog:

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

v8.8:

  • iProphet for peptide level reports.
  • Moved all downstream tools (Peptide/Protein Prophet, Crystal-C) to a single tab.
  • Simplified reports tab.
  • Ask twice about loading defaults automatically.
  • Removed decoy tag specification from command line fields. It's now always added implicitly.
Assets 4

Windows users

  • 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.
  • Or download the .jar file.
    • You can start the jar file with java -jar FragPipe-8.7.jar or start javaw -jar FragPipe-8.7.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

Download the .jar file and run with java -jar FragPipe-8.7.jar.

FragPipe v8.7 changelog:

v8.7:

  • Support for new Philosopher 20181119, Report Abacus --protein flag.

v8.6:

  • Updated nonspecific search default options.
  • Colorized console output.
  • Multiple UI fixes and updates.

v8.5:

  • Updated spectral library generation. LCMS files are copied and deleted from the right locations.
  • Multi-experiment protein level report.
  • Multi-experiment quantitation
  • Allow separate processing of input files one-by-one.

v8.4:

  • Combined protein report for multiple file groups.

v8.3:

  • LCMS files can be processed in separate groups.
  • Python detection on Windows via registry.
  • Python binary location can be specified manually.

v8.1:

  • DIA-Umpire SE added as an optional component. Mark the checkbox on Config panel to enable.

v8.0:

  • Added MSAdjuster, Crystal-C. Both packaged with the release, no extra downloads.

v7.2:

  • Added database slicing via a python script (Requires Python 3, NumPy, Pandas).

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.
Assets 4

Windows users

  • 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.
  • Or download the .jar file.
    • You can start the jar file with java -jar FragPipe-8.6.jar or start javaw -jar FragPipe-8.6.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

Download the .jar file and run with java -jar FragPipe-8.6.jar.

FragPipe v8.6 changelog:

v8.6:

  • Updated nonspecific search default options.
  • Colorized console output.
  • Multiple UI fixes and updates.

v8.5:

  • Updated spectral library generation. LCMS files are copied and deleted from the right locations.
  • Multi-experiment protein level report.
  • Multi-experiment quantitation
  • Allow separate processing of input files one-by-one.

v8.4:

  • Combined protein report for multiple file groups.

v8.3:

  • LCMS files can be processed in separate groups.
  • Python detection on Windows via registry.
  • Python binary location can be specified manually.

v8.1:

  • DIA-Umpire SE added as an optional component. Mark the checkbox on Config panel to enable.

v8.0:

  • Added MSAdjuster, Crystal-C. Both packaged with the release, no extra downloads.

v7.2:

  • Added database slicing via a python script (Requires Python 3, NumPy, Pandas).

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.
Assets 4
Nov 16, 2018
Bump to 8.5-RC9
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