Difference between revisions of "ABySS"
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|{{#vardefine:url|http://www.bcgsc.ca/platform/bioinfo/software/abyss}} | |{{#vardefine:url|http://www.bcgsc.ca/platform/bioinfo/software/abyss}} | ||
<!--Compiler and MPI settings - OPTIONAL --> | <!--Compiler and MPI settings - OPTIONAL --> | ||
| − | |{{#vardefine:intel|}} <!-- E.g. "11.1" --> | + | |{{#vardefine:intel|11.1}} <!-- E.g. "11.1" --> |
| − | |{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" --> | + | |{{#vardefine:mpi|openmpi/1.4.3}} <!-- E.g. "openmpi/1.3.4" --> |
<!--Choose sections to enable - OPTIONAL--> | <!--Choose sections to enable - OPTIONAL--> | ||
|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules --> | |{{#vardefine:mod|1}} <!--Present instructions for running the software with modules --> | ||
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{{App_Location|app={{#var:app}}|{{#var:ver}}}} | {{App_Location|app={{#var:app}}|{{#var:ver}}}} | ||
==Available versions== | ==Available versions== | ||
| − | * 1.3.1 - single threaded | + | * 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== | {{#if: {{#var: mod}}|==Running the application using modules== | ||
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* HPC_ABYSS_DOC - documents directory | * HPC_ABYSS_DOC - documents directory | ||
* HPC_ABYSS_MAN - manpages 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== | {{#if: {{#var: exe}}|==How To Run== | ||
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
Revision as of 16:35, 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:
Get module information for abyss:
$module spider abyss
Load Intel compiler:
$module load intel/11.1
Load MPI implementation:
$module load openmpi/1.4.3
Load the default application module:
$module load abyss
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