Difference between revisions of "Fastx Toolkit"

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m (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==")
m (Text replacement - "#uppercase" to "uc")
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__NOEDITSECTION__
 
__NOEDITSECTION__
 
[[Category:Software]][[Category:Bioinformatics]]
 
[[Category:Software]][[Category:Bioinformatics]]
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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"
 
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{|
 
<!--Main settings - REQUIRED-->
 
 
|{{#vardefine:app|fastx_toolkit}}
 
|{{#vardefine:app|fastx_toolkit}}
 
|{{#vardefine:url|http://hannonlab.cshl.edu/fastx_toolkit/}}
 
|{{#vardefine:url|http://hannonlab.cshl.edu/fastx_toolkit/}}
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|{{#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:exe|}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 
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The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
 
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
 
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<!--Modules-->
==Installed Versions==
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==Environment Modules==
* 0.0.13.1
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
<!-- -->
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==System Variables==
{{#if: {{#var: mod}}|==Execution Environment and Modules==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
 
 
* HPC_FASTX_TOOLKIT_BIN - executable directory
 
* HPC_FASTX_TOOLKIT_BIN - executable directory
 
{{#if: {{#var: exe}}|==How To Run==
 
{{#if: {{#var: exe}}|==How To Run==
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{{#if: {{#var: pbs}}|==PBS Script Examples==
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: policy}}|==Usage policy==
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{{#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)|}}
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==

Revision as of 21:20, 6 December 2019

Description

fastx_toolkit website  

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

Environment Modules

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

System Variables

  • HPC_FASTX_TOOLKIT_DIR - installation directory
  • HPC_FASTX_TOOLKIT_BIN - executable directory