MZMine

Description

mzmine website

MZmine is an open-source framework for processing, visualization and analysis of mass spectrometry based molecular profile data. It is based on the original MZmine toolbox described in 2006 Bioinformatics publication.

Environment Modules

Run module spider mzmine to find out what environment modules are available for this application.

Environment Variables

• HPC_MZMINE_DIR - installation directory
• HPC_MZMINE_BIN - executable directory
• HPC_MZMINE_LIB - library directory
• HPC_MZMINE_MEM - heap memory limit

Additional Usage Information

mzMine can be run in a batch mode according to mzMine Manual by calling startMZmine with a single argument corresponding to a saved batch script generated within the GUI.

We provide an alternate startMZmine script that correctly sets the HEAP memory based on either the HPC_MZMINE_MEM environment variable or, if that variable if absent, based on the total amount of requested memory within a job. Also it appears to be necessary to simulate a virtual X11 environment for mzMine to run in batch mode.

Note that HiPerGator2 nodes are diskless, so /tmp directory that mzMine uses by default for its temporary files cannot be used. See Temporary Directories for details on how to set $TMPDIR variable that points to a directory in your /blue space.

If you need to run mzMine GUI, you should use OOD and the HiPerGator Desktop application.

Categories

biology, spectroscopy