Difference between revisions of "FragGeneScan"

Revision as of 17:15, 23 April 2012

Description

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FragGeneScan is an application for finding (fragmented) genes in short reads. Template:App Location

Available versions

1.16.

Running the application using modules

To use fraggenescan with the environment modules system at HPC the following commands are available:

Get module information for fraggenescan:

$module spider fraggenescan

Load the default application module:

$module load fraggenescan

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

HPC_FRAGGENESCAN_DIR - directory where fraggenescan is located.
HPC_FRAGGENESCAN_BIN - executable directory.

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

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 * HPC_FRAGGENESCAN_BIN - executable directory.
 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
 |}}