fragpipe on Biowulf

FragPipe is a Java Graphical User Interface (GUI) and CLI workflow tool for a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data. It is powered by MSFragger - an ultrafast proteomic search engine suitable for both conventional and “open” (wide precursor mass tolerance) peptide identification.

Important Notes

GUI use of this application requires a graphical connection using NX

Interactive job
The fragpipe GUI must be run in an Interactive job. The underlying programs that it uses like msfragger and philosopher can be run as batch or swarm jobs.

First, start a nomachine desktop session on the Biowulf login node. Within your nx session, allocate an interactive session and run fragpipe.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load fragpipe

[user@cn3144 ~]$ fragpipe

You should now see the Java Graphical User Interface (GUI).

fragpipe image

If you run fragpipe from this central location, you will be unable to save data (like newly created pipelines) and recover them in a new session. You can copy fragpipe to your own space using the following commands or similar:

[user@cn3144]$ module load fragpipe

[user@cn3144]$ export INSTALL_DIR=/data/${USER}/fragpipe

[user@cn3144]$ mkdir -p $INSTALL_DIR && cd $INSTALL_DIR

[user@cn3144]$ tar xvf $FRAGPIPE_TAR

These steps need only be carried out once. In future sessions fragpipe will already be installed in your space. You can now run it using the full path (where <ver> is the version of fragpipe that you copied).

[user@cn3144]$ /data/${USER}/fragpipe/<ver>/bin/fragpipe

Or you can add the directory to your path to open more easily:

[user@cn3144]$ export PATH=/data/${USER}/fragpipe/<ver>/bin:$PATH

[user@cn3144]$ fragpipe
In either case, your saved data will now persist across sessions. When running fragpipe from your own space, it's still a good idea to load the fragpipe module first to properly prepare your environment.
Batch job
Most jobs should be run as batch jobs.

FragPipe versions 18.0+ may now be run in headless mode to submit as part of an interactive or batch job.

Workflow and manifest files should be created using the GUI either in an interactive session or on your own computer.

fragpipe headless config

Create a batch input file (e.g. For example:

set -e
module load fragpipe/18.0
cd /path/to/data/and/conf

fragpipe --headless \
  --workflow <path to workflow file> \
  --manifest <path to manifest file> \
  --workdir <path to result directory>