Difference between revisions of "FragGeneScan"

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m (Text replace - "{{#if: {{#var: mod}}|==Execution Environment and Modules== {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}" to "==Required Modules== modules documentation ===Serial=== *{{#var:app}}")
 
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__NOTOC__
 
__NOTOC__
 
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[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
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[[Category:Software]][[Category:Biology]][[Category:Genomics]]
<!-- ########  Template Configuration ######## -->
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{|<!--Main settings - REQUIRED-->
<!--Edit definitions of the variables used in template calls
 
Required variables:
 
app - lowercase name of the application e.g. "amber"
 
url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
 
Optional variables:
 
INTEL - Version of the Intel Compiler e.g. "11.1"
 
MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
 
-->
 
{|
 
<!--Main settings - REQUIRED-->
 
 
|{{#vardefine:app|fraggenescan}}
 
|{{#vardefine:app|fraggenescan}}
 
|{{#vardefine:url|http://omics.informatics.indiana.edu/FragGeneScan/}}
 
|{{#vardefine:url|http://omics.informatics.indiana.edu/FragGeneScan/}}
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|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
<!--Choose sections to enable - OPTIONAL-->
 
|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
 
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FragGeneScan is an application for finding (fragmented) genes in short reads.
 
FragGeneScan is an application for finding (fragmented) genes in short reads.
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
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==Environment Modules==
[[Modules|modules documentation]]
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
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==System Variables==
*{{#var:app}}
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_FRAGGENESCAN_BIN - executable directory.
 
* HPC_FRAGGENESCAN_BIN - executable directory.
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<!--Additional-->
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{{#if: {{#var: exe}}|==Additional Information==
 
Two convenience scripts are provided within the FragGeneScan distribution - run_FragGeneScan.pl and post_process.pl -  in addition to the main FragGeneScan binary.
 
Two convenience scripts are provided within the FragGeneScan distribution - run_FragGeneScan.pl and post_process.pl -  in addition to the main FragGeneScan binary.
  
 
Read the [http://omics.informatics.indiana.edu/FragGeneScan/README usage documentation] for details on how to run the program.
 
Read the [http://omics.informatics.indiana.edu/FragGeneScan/README usage documentation] for details on how to run the program.
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}}
 
{{#if: {{#var: citation}}|==Citation==
 
{{#if: {{#var: citation}}|==Citation==
 
Mina Rho, Haixu Tang, and Yuzhen Ye. FragGeneScan: Predicting Genes in Short and Error-prone Reads. Nucl. Acids Res., 2010 doi: [http://nar.oxfordjournals.org/content/early/2010/08/29/nar.gkq747.abstract 10.1093/nar/gkq747]
 
Mina Rho, Haixu Tang, and Yuzhen Ye. FragGeneScan: Predicting Genes in Short and Error-prone Reads. Nucl. Acids Res., 2010 doi: [http://nar.oxfordjournals.org/content/early/2010/08/29/nar.gkq747.abstract 10.1093/nar/gkq747]
 
|}}
 
|}}

Latest revision as of 16:48, 15 August 2022

Description

fraggenescan website  

FragGeneScan is an application for finding (fragmented) genes in short reads.

Environment Modules

Run module spider fraggenescan to find out what environment modules are available for this application.

System Variables

  • HPC_FRAGGENESCAN_DIR - installation directory
  • HPC_FRAGGENESCAN_BIN - executable directory.

Additional Information

Two convenience scripts are provided within the FragGeneScan distribution - run_FragGeneScan.pl and post_process.pl - in addition to the main FragGeneScan binary.

Read the usage documentation for details on how to run the program.

Citation

Mina Rho, Haixu Tang, and Yuzhen Ye. FragGeneScan: Predicting Genes in Short and Error-prone Reads. Nucl. Acids Res., 2010 doi: 10.1093/nar/gkq747