BIOMART: Difference between revisions

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.

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Biology]][[Category:Genomics]]
+[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|biomart}}
@@ Line 5: / Line 5: @@
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
-|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
+|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
-|{{#vardefine:job|}}            <!--JOB SCRIPTS-->
+|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
 |{{#vardefine:testing|}}       <!--PROFILING-->
@@ Line 18: / Line 18: @@
 {{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-->
-==Environment Modules==
+==Required Modules==
-Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
+===Serial===
+* {{#var:app}}
+<!--
+===Parallel (OpenMP)===
+* intel
+* {{#var:app}}
+===Parallel (MPI)===
+* intel
+* openmpi
+* {{#var:app}}
+-->
 ==System Variables==
 * HPC_{{uc:{{#var:app}}}}_DIR - installation directory
@@ Line 34: / Line 46: @@
 {{#if: {{#var: exe}}|==Additional Information==
-WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+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.
 |}}
-<!--Job Scripts-->
+<!--PBS scripts-->
-{{#if: {{#var: job}}|==Job Script Examples==
+{{#if: {{#var: pbs}}|==PBS Script Examples==
-See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.
+See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.
 |}}
 <!--Policy-->