Difference between revisions of "FragGeneScan"

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

@@ Line 1: / Line 1: @@
 __NOTOC__
 __NOEDITSECTION__
-[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
+[[Category:Software]][[Category:Biology]][[Category:Genomics]]
-<!-- ########  Template Configuration ######## -->
+{|<!--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:url|http://omics.informatics.indiana.edu/FragGeneScan/}}
-<!--Compiler and MPI settings - OPTIONAL -->
+|{{#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:pbs|}} <!--Enable PBS script wiki page link-->
@@ Line 26: / Line 11: @@
 |{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
 |{{#vardefine:faq|}} <!--Enable FAQ section -->
-|{{#vardefine:citation|}} <!--Enable Reference/Citation section -->
+|{{#vardefine:citation|1}} <!--Enable Reference/Citation section -->
 |}
 <!-- ########  Template Body ######## -->
 <!--Description-->
 {{#if: {{#var: url}}|
-{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
+{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 FragGeneScan is an application for finding (fragmented) genes in short reads.
-<!--Location-->
+<!--Modules-->
-{{App_Location|app={{#var:app}}|{{#var:ver}}}}
+==Environment Modules==
-==Available versions==
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-* 1.16.
+==System Variables==
-<!-- -->
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-{{#if: {{#var: mod}}|==Running the application using modules==
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
 * HPC_FRAGGENESCAN_BIN - executable directory.
+<!--Additional-->
+{{#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.
-{{#if: {{#var: exe}}|==How To Run==
-WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
+Read the [http://omics.informatics.indiana.edu/FragGeneScan/README usage documentation] for details on how to run the program.
-{{#if: {{#var: conf}}|==Configuration==
+}}
-See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
-{{#if: {{#var: pbs}}|==PBS Script Examples==
-See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
-{{#if: {{#var: policy}}|==Usage policy==
-WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
-{{#if: {{#var: testing}}|==Performance==
-WRITE PERFORMANCE TESTING RESULTS HERE|}}
-{{#if: {{#var: faq}}|==FAQ==
-*'''Q:''' **'''A:'''|}}
 {{#if: {{#var: citation}}|==Citation==
-If you publish research that uses {{{app}}} you have to cite it as follows:
+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]
-WRITE CITATION HERE
 |}}