FragPipe (previously - MSfragger GUI)

This is a very basic Java GUI wrapper for MSFragger - ultrafast proteomic search engine.
It will help you launch MSFragger for Open and Closed searches and can also run post-processing of results with Peptide/Protein Prophets as well as generate tabular summary results using Philosopher.

Download

Download precompiled binaries from the Releases section of this repository

Running

• on Windows use one of the following:
  • Run the Windows executable (.exe)
  • Run the .bat file included in the release zip file
  • start javaw -jar MSfragger-GUI.jar
  • java -jar MSfragger-GUI.jar
• Linux/MacOS
  • Run the shell script included in the release zip file
  • java -jar MSfragger-GUI.jar

Referencing the work

Please cite the following paper:
Andy Kong, Felipe Leprevost, Dmitry Avtonomov, Dattatreya Mellacheruvu, Alexey Nesvizhskii. "MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics". Nat Meth, May 2017. DOI: 10.1038/nmeth.4256

Building

With Gradle (preferred)

You don't need to have Gradle installed. This method uses Gradle Wrapper, which is included in this repository. Eeverything needed for the build will be downloaded.

• To get the jar with all dependencies included, from the directory with the gradle.build file:
  ./gradlew clean shadowJar

• If you're on Windows you can also build a Windows binary:
  ./gradlew clean createAllExecutables

• To create a zip file with the jar and startup scripts/bat files:
  ./gradlew distZip

Inspect the output in MSFragger-GUI/build/lbis and MSFragger-GUI/build/distributions folders.

With NetBeans (Ant build, actually)

Open the source project in NetBeans and do "Clean Build". You will get the jar in ./dist directory and a zip file with the current version in the file name and start scripts bundled.

Updating build version

The version of the build is stored in 2 separate places:

• MSFragger-GUI/src/umich/msfragger/Version.java
  • VERSION static field
• MSFragger-GUI/src/umich/msfragger/gui/Bundle.properties
  • msfragger.gui.version property Both need to be modified to the same value, otherwise you'll get a popup warning at the start of the application.

Also don't forget to update the version in build.gradle.