Difference between revisions of "MZMine"
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
| − | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | + | |{{#vardefine:pbs|1}} <!--PBS SCRIPTS--> |
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
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<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
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| + | mzMine can be run in a batch mode according to [https://docs.google.com/document/d/1JtdNwp1y6wz_Boz8qVGESH-kSrMhcGaJWR18iGmhstU/edit 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. | ||
|}} | |}} | ||
<!--PBS scripts--> | <!--PBS scripts--> | ||
Revision as of 15:51, 14 December 2015
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.
PBS Script Examples
See the MZMine_PBS page for mzmine PBS script examples.