Difference between revisions of "InterProScan"
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Moskalenko (talk | contribs) m (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|iprscan}} | |{{#vardefine:app|iprscan}} | ||
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|{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice --> | |{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice --> | ||
|{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice --> | |{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice --> | ||
| − | |{{#vardefine:exe|}} <!--RUNNING --> | + | |{{#vardefine:exe|1}} <!--RUNNING --> |
|{{#vardefine:conf|}} <!--CONFIGS--> | |{{#vardefine:conf|}} <!--CONFIGS--> | ||
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | This software allows you to query your sequence against the InterPro databases. | + | This interproscan software allows you to query your sequence against the InterPro databases. |
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<!--Modules--> | <!--Modules--> | ||
| − | + | ==Environment Modules== | |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | + | ==System Variables== | |
| + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
<!--Run--> | <!--Run--> | ||
| + | |||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
| − | + | ||
| + | Interproscan 5 series is run differently from the "4.x" series. See [https://code.google.com/p/interproscan/wiki/i5RC6HowToRun https://code.google.com/p/interproscan/wiki/i5RC6HowToRun] for details or load the module and run "interproscan.sh". To set the amount of memory Interproscan can use set the "_JAVA_OPTIONS" variable to a value different from the default 2048M, e.g. '<code>$ export _JAVA_OPTIONS="-Xmx8192M"</code>' | ||
|}} | |}} | ||
<!--Configuration--> | <!--Configuration--> | ||
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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
<!--Policy--> | <!--Policy--> | ||
| − | {{#if: {{#var: policy}}|==Usage | + | {{#if: {{#var: policy}}|==Usage Policy== |
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used) | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used) | ||
|}} | |}} | ||
Latest revision as of 19:23, 12 August 2022
Description
This interproscan software allows you to query your sequence against the InterPro databases.
Environment Modules
Run module spider iprscan to find out what environment modules are available for this application.
System Variables
- HPC_IPRSCAN_DIR - installation directory
How To Run
Interproscan 5 series is run differently from the "4.x" series. See https://code.google.com/p/interproscan/wiki/i5RC6HowToRun for details or load the module and run "interproscan.sh". To set the amount of memory Interproscan can use set the "_JAVA_OPTIONS" variable to a value different from the default 2048M, e.g. '$ export _JAVA_OPTIONS="-Xmx8192M"'