Difference between revisions of "Bamtools"

From UFRC
Jump to navigation Jump to search
Line 42: Line 42:
 
* HPC_BAMTOOLS_BIN - executable directory
 
* HPC_BAMTOOLS_BIN - executable directory
 
* HPC_BAMTOOLS_INC - includes directory
 
* HPC_BAMTOOLS_INC - includes 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==
 
{{#if: {{#var: exe}}|==How To Run==
 
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
 
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}

Revision as of 23:06, 27 January 2012

Description

{{{name}}} website  
BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files. Template:App Location

Available versions

  • 2.1.0

Running the application using modules

To use bamtools with the environment modules system at HPC the following commands are available:

Get module information for bamtools:

$module spider bamtools

Load the default application module:

$module load bamtools

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

  • HPC_BAMTOOLS_DIR - directory where bamtools is located.
  • HPC_BAMTOOLS_BIN - executable directory
  • HPC_BAMTOOLS_INC - includes 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) - [