Difference between revisions of "BIOMART"
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(Created page with "Category:SoftwareCategory:BiologyCategory:Genomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|biomart}} |{{#vardefine:url|http://useast.ensembl.org/info/da...") |
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<!--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: | + | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> |
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
| Line 18: | Line 18: | ||
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | Tables of Ensembl data can be downloaded via the highly customisable BioMart data mining tool. The BioMart Perl API allow you to go a step further with BioMart and allow you to integrate BioMart Perl Code into custom Perl scripts. | + | Tables of Ensembl data can be downloaded via the highly customisable BioMart |
| + | data mining tool. The BioMart Perl API allow you to go a step further with | ||
| + | BioMart and allow you to integrate BioMart Perl Code into custom Perl scripts. | ||
<!--Modules--> | <!--Modules--> | ||
| Line 24: | Line 26: | ||
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | 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_{{uc:{{#var:app}}}}_BIN - executable directory | ||
| + | * HPC_{{uc:{{#var:app}}}}_CONF - configuration directory | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
| Line 32: | Line 36: | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | Download the default [http://useast.ensembl.org/biomart/martservice?type=registry BioMart Registry] and save it as an xml file to be used with the biomart API scripts. | |
|}} | |}} | ||
| − | <!-- | + | <!--PBS scripts--> |
| − | {{#if: {{#var: | + | {{#if: {{#var: pbs}}|==PBS Script Examples== |
| − | See the [[{{PAGENAME}} | + | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples. |
|}} | |}} | ||
<!--Policy--> | <!--Policy--> | ||
Latest revision as of 18:16, 12 August 2022
Description
Tables of Ensembl data can be downloaded via the highly customisable BioMart data mining tool. The BioMart Perl API allow you to go a step further with BioMart and allow you to integrate BioMart Perl Code into custom Perl scripts.
Environment Modules
Run module spider biomart to find out what environment modules are available for this application.
System Variables
- HPC_BIOMART_DIR - installation directory
- HPC_BIOMART_BIN - executable directory
- HPC_BIOMART_CONF - configuration directory
Additional Information
Download the default BioMart Registry and save it as an xml file to be used with the biomart API scripts.