HapCompass: Difference between revisions
Moskalenko (talk | contribs) No edit summary |
No edit summary |
||
| (5 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
[[Category:Software]][[Category: | [[Category:Software]][[Category:Genomics]][[Category:NGS]] | ||
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|hapcompass}} | |{{#vardefine:app|hapcompass}} | ||
| Line 5: | Line 5: | ||
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
|{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> | ||
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
| Line 22: | Line 22: | ||
<!--Modules--> | <!--Modules--> | ||
== | ==Environment Modules== | ||
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |||
< | |||
==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== | ||
| Line 45: | Line 35: | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
{{JAVA_OPTIONS}} | |||
|}} | |}} | ||
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....