Difference between revisions of "InterProScan"

Latest revision as of 19:23, 12 August 2022

Description

iprscan website

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"'

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Bioinformatics]]
+[[Category:Software]][[Category:Biology]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|iprscan}}
@@ Line 7: / Line 7: @@
 |{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice -->
 |{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice -->
-|{{#vardefine:exe|}} <!--RUNNING -->
+|{{#vardefine:exe|1}} <!--RUNNING -->
 |{{#vardefine:conf|}} <!--CONFIGS-->
 |{{#vardefine:pbs|}} <!--PBS SCRIPTS-->
@@ Line 21: / Line 21: @@
 {{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.
-<!--Versions-->
-==Available versions==
-* 4.8
 <!--Modules-->
-{{#if: {{#var: mod}}|==Running the application using modules==
+==Environment Modules==
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
+==System Variables==
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 <!--Run-->
 {{#if: {{#var: exe}}|==How To Run==
-DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY
+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-->
@@ Line 42: / Line 42: @@
 See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 <!--Policy-->
-{{#if: {{#var: policy}}|==Usage policy==
+{{#if: {{#var: policy}}|==Usage Policy==
 WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)
 |}}