Difference between revisions of "HapCompass"
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{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|hapcompass}} | |{{#vardefine:app|hapcompass}} | ||
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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== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DOC - documentation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_EXE - examples directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 18:13, 15 August 2022
Description
HapCompass implements a novel HAPCOMPASS algorithm for haplotype assembly of densely sequenced human genome data. The algorithm operates on a graph where SNPs are nodes and edges are defined by the sequencing reads and viewed as supporting evidence of co-occuring SNP alleles in a haplotype.
Environment Modules
Run module spider hapcompass to find out what environment modules are available for this application.
System Variables
- HPC_HAPCOMPASS_DIR - installation directory
- HPC_HAPCOMPASS_DOC - documentation directory
- HPC_HAPCOMPASS_EXE - examples directory
Additional Information
To set the heap memory to be used by a java program export the _JAVA_OPTIONS variable in the environment the program runs in - either on the command line, in a personal module, or in a job script. For example,
export _JAVA_OPTIONS="-Xms1g -Xmx4g"
will set Java heap memory usage to a minimum of 1g and a maximum of 4g. Please note that _JAVA_OPTIONS environment variable overrides the respective command-line arguments. For example, the above '_JAVA_OPTIONS' variable will override the '-Xmx500m' argument in
java -Xmx500m -jar someprogram.jar....