Difference between revisions of "ABySS"

Revision as of 16:58, 16 November 2011

Description

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ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes. Template:App Location

Available versions

1.3.1 - single threaded and MPI ( loading of intel/11.1 and openmpi/1.4.3 modules required)

Running the application using modules

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

(Note the warnings you get if you don't load the 'bowtie' and 'bwa' modules)

Single threaded version

Get module information for abyss:

$module spider abyss

Load the application module:

$module load abyss

MPI version

Load Intel compiler:

$module load intel/11.1

Load MPI implementation:

$module load openmpi/1.4.3

Load the application module:

$module load abyss

To load the single-threaded version of abyss after the MPI version was loaded purge the modules and load abyss module or simply unload the openmpi module and the abyss module will be reloaded to a single-threaded version automatically.

module purge
module load abyss

or

module unload openmpi

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

HPC_ABYSS_DIR - directory where abyss is located.
HPC_ABYSS_BIN - executable directory
HPC_ABYSS_DOC - documents directory
HPC_ABYSS_MAN - manpages directory

@@ Line 15: / Line 15: @@
 |{{#vardefine:app|abyss}}
 |{{#vardefine:url|http://www.bcgsc.ca/platform/bioinfo/software/abyss}}
-<!--Compiler and MPI settings - OPTIONAL -->
-|{{#vardefine:intel|11.1}} <!-- E.g. "11.1" -->
-|{{#vardefine:mpi|openmpi/1.4.3}} <!-- 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 38: / Line 34: @@
 * 1.3.1 - single threaded and MPI ( loading of intel/11.1 and openmpi/1.4.3 modules required)
 <!-- -->
-{{#if: {{#var: mod}}|==Running the application using modules==
+==Running the application using modules==
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+To use abyss with the environment modules system at HPC the following commands are available:
+'''(Note the warnings you get if you don't load the 'bowtie' and 'bwa' modules)'''
+===Single threaded version===
+Get module information for abyss:
+ $module spider abyss
+Load the application module:
+ $module load abyss
+===MPI version===
+Load Intel compiler:
+ $module load intel/11.1
+Load MPI implementation:
+ $module load openmpi/1.4.3
+Load the application module:
+ $module load abyss
+To load the single-threaded version of abyss after the MPI version was loaded purge the modules and load abyss module or simply unload the openmpi module and the abyss module will be reloaded to a single-threaded version automatically.
+ module purge
+ module load abyss
+or
+ module unload openmpi
+The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
+* HPC_ABYSS_DIR - directory where abyss is located.
 * HPC_ABYSS_BIN - executable directory
 * HPC_ABYSS_DOC - documents directory
 * HPC_ABYSS_MAN - manpages directory
-To load the single-threaded version of abyss purge the modules and load abyss module or simply unload the openmpi module and the abyss module will be switched to a single-threaded version automatically.
- module purge
- module load abyss
 {{#if: {{#var: exe}}|==How To Run==
 WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}