Difference between revisions of "Fastx Toolkit"
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Moskalenko (talk | contribs) (Created page with "__NOTOC__ __NOEDITSECTION__ Category:SoftwareCategory:Bioinformatics <!-- ######## Template Configuration ######## --> <!--Edit definitions of the variables used in temp...") |
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__NOTOC__ | __NOTOC__ | ||
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]] |
| − | + | {|<!--Main settings - REQUIRED--> | |
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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: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--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
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<!--Description--> | <!--Description--> | ||
{{#if: {{#var: url}}| | {{#if: {{#var: url}}| | ||
| − | {{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | + | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} |
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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. | ||
| − | <!-- | + | <!--Modules--> |
| − | + | ==Environment Modules== | |
| − | == | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. |
| − | + | ==System Variables== | |
| − | < | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
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| − | {{ | ||
* 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 | + | {{#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== | ||
Latest revision as of 16:37, 15 August 2022
Description
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