General Use Containers

This page provide brief information of containers available to all O2 users.

List of Containers

MaxQuant

A quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.

# Connect to O2
# Note: replace "PORT" by a random number in the 50000-range, e.g. 50021
ssh -Y -L PORT:127.0.0.1:PORT <your_hms_id>@o2.hms.harvard.edu

# start an interactive job (e.g., requesting 1 hour, 4 threads, and 10GB)
# Note: Replace "PORT" with the choosed number in the above step
srun -t 0-1 --x11 --pty -p interactive -c 4 --mem=10G --tunnel PORT:PORT /bin/bash

# Run the MaxQuant container
SIF_PATH="/n/app/singularity/containers/hmsrc-maxquant.sif"
singularity run -B "$TMPDIR:/tmp",/n --app MaxQuantGui.exe $SIF_PATH

To use MaxQuant from the terminal:

SIF_PATH="/n/app/singularity/containers/hmsrc-maxquant.sif"
singularity run -B "$TMPDIR:/tmp",/n --app MaxQuantCmd.exe mqpar.xml $SIF_PATH

Note: the mqpar.xml file is where you specify all the information related to the data analysis.