Difference between revisions of "MZMine"
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|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
|{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> | ||
| − | |{{#vardefine: | + | |{{#vardefine:job|}} <!--JOB SCRIPTS--> |
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
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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. | 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. | ||
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| − | <!-- | + | <!--JOBscripts--> |
| − | {{#if: {{#var: | + | {{#if: {{#var: job}}|==Job Script Examples== |
| − | See the [[{{PAGENAME}} | + | See the [[{{PAGENAME}}_Job_Script]] page for {{#var: app}} job script examples. |
|}} | |}} | ||
<!--Policy--> | <!--Policy--> | ||
Revision as of 04:09, 3 August 2016
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.