MZMine

Description

mzmine website
MZmine 2 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.

Required Modules

Serial

mzmine

System Variables

HPC_{{#uppercase:mzmine}}_DIR - installation directory

Additional 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. Pleas see the sample script below. Note that 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 /ufrc space.

If you need to run mzMine GUI you have to run it in a gui session under SLURM and use Xpra software to connect to the session. See our Xpra on HiPerGator documentation for reference.

Example session:

[jdoe@gator3 mzmine]$ module load mzmine

Let's try the launcher script to star mzMine in a gui session under SLURM and wrap it in Xpra, so we could connect from the outside. Here's the help message when you get if you use the '-h' argument'

[jdoe@gator3 mzmine]$ launch_xpra_mzmine -h

Usage:

        launch_xpra_mzmine [options]

Options:

        -h - show this help message

        -m <value> - memory, gb (default is 4gb)

        -a <value> - SLURM account (default is your main account)

        -b - Use burst SLURM qos (default is main qos)

        -t <value> - SLURM time limit, hrs (default is 4hrs)


All arguments are optional. Defaults will be used for missing values

Alright, let's do a test run. Let's say you wanted to use 6gb of memory and run mzmine for 24 hours.

[jdoe@gator3 test_directory]$ launch_xpra_mzmine -m 6 -t 24

Starting mzMine under Xpra in a SLURM gui session.

Requested mzMine memory size: '6gb'

Submitted batch job 815185

Run: 'xpra_list_sessions' after job starts to see the connection command

See https://wiki.rc.ufl.edu/doc/Xpra for documentation

             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
            815185       gui   mzmine   jdoe   R       0:10      1 aaa-bbb

Refreshing the session list for jdoe to remove stale sessions
Warning: Permanently added 'aaa-bbb.ufhpc,123.45.678.9' (RSA) to the list of known hosts.

Xpra session status for jdoe have been refreshed.

Xpra sessions for jdoe:
    aaa-bbb.rc.ufl.edu:7176
        Connection command: xpra attach ssh:jdoe@aaa-bbb.rc.ufl.edu:7176

Since the job already started we already see a live Xpra session in the above output. Otherwise, we'd have to wait for the jbo to start and then run xpra_list_sessions (load 'gui' module if needed to acces the command).

Let's connect to UF VPN (https://kb.helpdesk.ufl.edu/FAQs/VPNInstructions) and then use the xpra script from https://wiki.rc.ufl.edu/doc/Xpra#Microsoft_Windows in a MobaXTerm terminal on a windows client machine (for example). If you run

sh xpra attach ssh:jdoe@aaa-bbb.rc.ufl.edu:7176

in MobaXTerm you should see a password window from TortoisePlink. After you enter the password you should see the mzMine GUI show up on your local machine. Do not close the program with the [x] close button in the right-top corner of mzMine GUI window unless you want the job to complete. Click on the MobaXTerm terminal where you started the command and use 'Ctrl+c" key combination to detach from the session, so you could re-attach later.

PBS Script Examples

See the MZMine_PBS page for mzmine PBS script examples.