Difference between revisions of "Bamtools"
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Moskalenko (talk | contribs) m (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==") |
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__NOTOC__ | __NOTOC__ | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:NGS]][[Category:Biology]][[Category:Sequencing]] |
| − | + | {|<!--Main settings - REQUIRED--> | |
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| − | {| | ||
| − | <!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|bamtools}} | |{{#vardefine:app|bamtools}} | ||
|{{#vardefine:url|https://github.com/pezmaster31/bamtools/wiki}} | |{{#vardefine:url|https://github.com/pezmaster31/bamtools/wiki}} | ||
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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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BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files. | BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files. | ||
| − | + | <!--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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==Additional tools== | ==Additional tools== | ||
We also provide small tools that depend on bamtools or are built against it within this module. | We also provide small tools that depend on bamtools or are built against it within this module. | ||
* [https://github.com/ekg/bamaddrg bamaddrg] (2012-01-27 build against bamtools 0.9.4). | * [https://github.com/ekg/bamaddrg bamaddrg] (2012-01-27 build against bamtools 0.9.4). | ||
| − | {{#if: {{#var: exe}}|== | + | <!--Additional--> |
| + | {{#if: {{#var: exe}}|==Additional Information== | ||
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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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 18:02, 12 August 2022
Description
BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files.
Environment Modules
Run module spider bamtools to find out what environment modules are available for this application.
System Variables
- HPC_BAMTOOLS_DIR - installation directory
Additional tools
We also provide small tools that depend on bamtools or are built against it within this module.
- bamaddrg (2012-01-27 build against bamtools 0.9.4).