This page provide brief information of containers available to all O2 users.
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MaxQuant
A quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.
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# 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 $SIF_PATH |
To use MaxQuant from the terminal:
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SIF_PATH="/n/app/singularity/containers/hmsrc-maxquant.sif" singularity run -B "$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.