Difference between revisions of "BIOMART"
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Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|biomart}} | |{{#vardefine:app|biomart}} | ||
| 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: | + | |{{#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--> | ||
| − | == | + | ==Required Modules== |
| − | + | ===Serial=== | |
| + | * {{#var:app}} | ||
| + | <!-- | ||
| + | ===Parallel (OpenMP)=== | ||
| + | * intel | ||
| + | * {{#var:app}} | ||
| + | ===Parallel (MPI)=== | ||
| + | * intel | ||
| + | * openmpi | ||
| + | * {{#var:app}} | ||
| + | --> | ||
==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| Line 34: | Line 46: | ||
{{#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--> | ||
Revision as of 16:17, 27 May 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.
Required Modules
Serial
- biomart
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.