Difference between revisions of "BioBakery"
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(Created page with "Category:SoftwareCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|biobakery}} |{{#vardefine:url|https://bitbucket.org/biobakery/biobakery`}} <...") |
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{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|biobakery}} | |{{#vardefine:app|biobakery}} | ||
| − | |{{#vardefine:url| | + | |{{#vardefine:url|http://huttenhower.sph.harvard.edu/biobakery_workflows}} |
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | + | BioBakery Workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters. Quality control and statistical summary reports are automatically generated for most data types, which include 16S amplicons, metagenomes, and metatranscriptomes. | |
<!--Modules--> | <!--Modules--> | ||
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
| + | * BIOBAKERY_WORKFLOWS_DATABASES - reference database | ||
<!--Configuration--> | <!--Configuration--> | ||
Latest revision as of 14:04, 3 February 2022
Description
BioBakery Workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters. Quality control and statistical summary reports are automatically generated for most data types, which include 16S amplicons, metagenomes, and metatranscriptomes.
Environment Modules
Run module spider biobakery to find out what environment modules are available for this application.
System Variables
- HPC_BIOBAKERY_DIR - installation directory
- HPC_BIOBAKERY_BIN - executable directory
- BIOBAKERY_WORKFLOWS_DATABASES - reference database