Release FragPipe v19.0 · Nesvilab/FragPipe

Downloading

The zip (FragPipe-19.0.zip) doesn't contain Java, you will need Java 9+ to run.
The other zip with -jre- in its name (FragPipe-jre-19.0.zip) contains a Java runtime for Windows only.

Unzip the file
In /bin subdirectory you will find a shell script for Linux, bat file for Windows, and an exe file for Windows

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.

v19.0:

Require Java 9+
Require MSFragger 3.6+
Require Philosopher 4.6.0+
Require IonQuant 1.8.9+
Require EasyPQP 0.1.34+
Add O-Pair for O-Glycan localization
Add downstream analysis tool SAINT
Support PTM localization using PTMProphet for timsTOF .d and Thermo .raw formats
Add --config-ionquant flag in headless mode
Add "delete calibrated mzML" and "delete temp files" checkboxes
Add "open FragPipe-Analyst" button
Add "remove contaminants" checkbox to the "FDR filter and report" panel
Add "neutral loss" checkbox to the speclib tab
Add glycan database loader to Glyco tab
Add mass-offset list loader to MSFragger tab
Put DIA-NN's output fies to "diann-output" folder
Put EasyPQP output files to "eaasypqp_files" directory
Rename "Open visualization window" button to "Open FragPipe-PDV viewer"
Remove "Close visualization window" button
Write all TMT annotations to a single combined_annotation.txt file
Upgrade DIA-NN to 1.8.2 beta 8
Upgrade PTM-Shepherd to 2.0.3
Upgrade TMT-Integrator to 4.0.4
Upgrade DIA-Umpire to 2.3.1
Upgrade MSBooster to 1.1.10
Upgrade FP-PDV to 1.0.5
Add more workflows
Various minor bug fixes and improvements