Difference between revisions of "HapCompass"

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[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
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[[Category:Software]][[Category:Genomics]][[Category:NGS]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|hapcompass}}
 
|{{#vardefine:app|hapcompass}}
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<!--Modules-->
 
<!--Modules-->
==Required Modules==
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==Environment Modules==
===Serial===
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{#uppercase:{{#var:app}}}}_DOC - documentation directory
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* HPC_{{uc:{{#var:app}}}}_DOC - documentation directory
* HPC_{{#uppercase:{{#var:app}}}}_EXE - examples directory
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* 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 website  

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....