Difference between revisions of "MZMine"
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Spectroscopy]][[Category:Biology]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|mzmine}} | |{{#vardefine:app|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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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. | 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. | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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| − | < | ||
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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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. | 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. | ||
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| + | Note that HiPerGator2 nodes are diskless, so '<code>/tmp</code>' 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. | ||
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| + | If you need to run mzMine GUI, you should use [[GUI Programs|OOD and the HiPerGator Desktop application]]. | ||
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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--> | ||
Latest revision as of 13:28, 7 July 2023
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.
Environment Modules
Run module spider mzmine to find out what environment modules are available for this application.
System Variables
- HPC_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 /blue space.
If you need to run mzMine GUI, you should use OOD and the HiPerGator Desktop application.