Difference between revisions of "Bamtools"

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).

@@ Line 1: / Line 1: @@
 __NOTOC__
 __NOEDITSECTION__
-[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
+[[Category:Software]][[Category:NGS]][[Category:Biology]][[Category:Sequencing]]
-<!-- ########  Template Configuration ######## -->
+{|<!--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"
--->
-{|
-<!--Main settings - REQUIRED-->
 |{{#vardefine:app|bamtools}}
 |{{#vardefine:url|https://github.com/pezmaster31/bamtools/wiki}}
-<!--Compiler and MPI settings - OPTIONAL -->
-|{{#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:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
@@ Line 36: / Line 21: @@
 <!--Modules-->
-{{#if: {{#var: mod}}|==Execution Environment and Modules==
+==Environment Modules==
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-* HPC_BAMTOOLS_BIN - executable directory
+==System Variables==
-* HPC_BAMTOOLS_INC - includes directory
+* 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}}|==How To Run==
+<!--Additional-->
+{{#if: {{#var: exe}}|==Additional Information==
 WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 49: / Line 35: @@
 {{#if: {{#var: pbs}}|==PBS Script Examples==
 See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
-{{#if: {{#var: policy}}|==Usage policy==
+{{#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==