Purdue University

Commands

• MaxQuantGui.exe
• MaxQuantCmd.exe

Module

You can load the modules by:

module load biocontainers
module load maxquant

GUI

To run Maxquant with GUI, it is recommended to run within ThinLinc:

(base) UserID@bell-fe00:~ $ sinteractive -N1 -n12 -t4:00:00 -A myallocation
salloc: Granted job allocation 12345869
salloc: Waiting for resource configuration
salloc: Nodes bell-a008 are ready for job
(base) UserID@bell-a008:~ $ module load biocontainers maxquant
(base) UserID@bell-a008:~ $ MaxQuantGui.exe

CMD job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Maxquant without GUI on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=maxquant
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers maxquant

MaxQuantCmd.exe mqpar.xml