FragPipe v11.0
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-11.0.zip.
- Zip contains
FragPipe.bat
file, which can be started by either clicking or running it from the command line.
- Zip contains
- Or download the FragPipe-11.0.jar.
- You can start the
jar
file withjava -jar FragPipe-11.0.jar
orstart javaw -jar FragPipe-11.0.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.
- You can start the
Linux/MacOS users
- Either download FragPipe-11.0.zip, which contains FragPipe shell script to start the program
- Or download the FragPipe-11.0.jar and run with
java -jar FragPipe-11.0.jar
.
Changelog:
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.