Difference between revisions of "Bamtools"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) |
|||
(17 intermediate revisions by 3 users not shown) | |||
Line 1: | Line 1: | ||
__NOTOC__ | __NOTOC__ | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
− | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:NGS]][[Category:Biology]][[Category:Sequencing]] |
− | + | {|<!--Main settings - REQUIRED--> | |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | {| | ||
− | <!--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}} | ||
− | |||
− | |||
− | |||
− | |||
− | |||
|{{#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--> | ||
Line 31: | Line 16: | ||
<!--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}}}}|}} |
+ | |||
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 | |
− | {{ | + | ==Additional tools== |
− | * | + | 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). | |
− | {{#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== | ||
Line 48: | Line 35: | ||
{{#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).