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.