Difference between revisions of "ABySS"

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m (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==")
 
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__NOTOC__
 
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[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
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[[Category:Software]][[Category:Biology]][[Category:De Novo]]
<!-- ########  Template Configuration ######## -->
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{|<!--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|abyss}}
 
|{{#vardefine:app|abyss}}
 
|{{#vardefine:url|http://www.bcgsc.ca/platform/bioinfo/software/abyss}}
 
|{{#vardefine:url|http://www.bcgsc.ca/platform/bioinfo/software/abyss}}
 
<!--Choose sections to enable - OPTIONAL-->
 
<!--Choose sections to enable - OPTIONAL-->
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
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|{{#vardefine:exe|1}} <!--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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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.
 
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.
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<!--Modules-->
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==Environment Modules==
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
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==System Variables==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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{{#if: {{#var: exe}}|==How To Run==
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The abyss-pe is hardcoded to use mpiexec, so you need to set the following variable in your abyss job script before calling abyss-pe to explicitly allow mpiexec usage, which is disabled by default:
  
==Available versions==
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  export HPC_USE_MPIEXEC=1
* 1.3.1 - single threaded and MPI ( loading of intel/11.1 and openmpi/1.4.3 modules required)
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|}}
* 1.3.4 - single threaded and MPI versions are provided. Load the abyss/1.4.3-mpi module for the latter version. All dependencies will autoload.
 
<!-- -->
 
==Execution Environment and Modules==
 
To use abyss with the environment modules system at HPC the following commands are available:
 
===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
 
'''Note:' since version 1.3.4 the MPI version can be loaded simply as
 
$module load abyss/1.3.4-mpi
 
 
 
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
 
 
 
{{#if: {{#var: exe}}|==How To Run==
 
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
 
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 
{{#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 policy==
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{{#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 16:17, 19 August 2022

Description

abyss website  

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.

Environment Modules

Run module spider abyss to find out what environment modules are available for this application.

System Variables

  • HPC_ABYSS_DIR - installation directory

How To Run

The abyss-pe is hardcoded to use mpiexec, so you need to set the following variable in your abyss job script before calling abyss-pe to explicitly allow mpiexec usage, which is disabled by default:

export HPC_USE_MPIEXEC=1