Difference between revisions of "MIRA"

Revision as of 16:48, 10 June 2022

Description

MIRA - Sequence assembler for whole genome shotgun and EST sequencing data. Can use Sanger, 454, Solexa (Illumina) and IonTorrent data. PacBio: CCS and ecCLR data usable, CLR not yet. Please visit the app website for more details.

Environment Modules

Run module spider mira to find out what environment modules are available for this application.

System Variables

HPC_MIRA_DIR - installation directory
HPC_MIRA_BIN - executable directory
HPC_MIRA_DOC - documentation directory

Documentation

The main documentation source for MIRA is the Definitive guide to MIRA.

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Biology]][[Category:Bioinformatics]][[Category:Genomics]][[Category:Assembly]]
+__NOTOC__
-{|<!--CONFIGURATION: REQUIRED-->
+__NOEDITSECTION__
+[[Category:Software]][[Category:Bioinformatics]]
+{|<!--Main settings - REQUIRED-->
 |{{#vardefine:app|mira}}
-|{{#vardefine:url|https://sourceforge.net/projects/mira-assembler/}}
+|{{#vardefine:url|http://mira-assembler.sourceforge.net/}}
-<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
+|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
-|{{#vardefine:conf|}}           <!--CONFIGURATION-->
+|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
-|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
+|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
-|{{#vardefine:job|}}            <!--JOB SCRIPTS-->
+|{{#vardefine:policy|}} <!--Enable policy section -->
-|{{#vardefine:policy|}}         <!--POLICY-->
+|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
-|{{#vardefine:testing|}}       <!--PROFILING-->
+|{{#vardefine:faq|}} <!--Enable FAQ section -->
-|{{#vardefine:faq|}}             <!--FAQ-->
+|{{#vardefine:citation|}} <!--Enable Reference/Citation section -->
-|{{#vardefine:citation|}}       <!--CITATION-->
-|{{#vardefine:installation|}} <!--INSTALLATION-->
 |}
-<!--BODY-->
+<!-- ########  Template Body ######## -->
 <!--Description-->
 {{#if: {{#var: url}}|
 {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
-MIRA - Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: CCS and error corrected data usable, uncorrected not yet.
+MIRA - Sequence assembler for whole genome shotgun and EST sequencing data. Can use Sanger, 454, Solexa (Illumina) and IonTorrent data. PacBio: CCS and ecCLR data usable, CLR not yet. Please visit [http://sourceforge.net/apps/mediawiki/mira-assembler/ the app website] for more details.
 <!--Modules-->
 ==Environment Modules==
 Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-* HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory
+* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
-* HPC_{{#uppercase:{{#var:app}}}}_DOC - documentation directory
+* HPC_{{uc:{{#var:app}}}}_DOC - documentation directory
+==Documentation==
-<!--Configuration-->
+The main documentation source for MIRA is the [http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html Definitive guide to MIRA].
+{{#if: {{#var: exe}}|==How To Run==
+WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
 {{#if: {{#var: conf}}|==Configuration==
-See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
+See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
-|}}
+{{#if: {{#var: pbs}}|==PBS Script Examples==
-<!--Run-->
+See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
-{{#if: {{#var: exe}}|==Additional Information==
-WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
-|}}
-<!--Job Scripts-->
-{{#if: {{#var: job}}|==Job Script Examples==
-See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.
-|}}
-<!--Policy-->
 {{#if: {{#var: policy}}|==Usage Policy==
+WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
-WRITE USAGE POLICY HERE (Licensing, usage, access).
-|}}
-<!--Performance-->
 {{#if: {{#var: testing}}|==Performance==
+WRITE PERFORMANCE TESTING RESULTS HERE|}}
-WRITE_PERFORMANCE_TESTING_RESULTS_HERE
-|}}
-<!--Faq-->
 {{#if: {{#var: faq}}|==FAQ==
 *'''Q:''' **'''A:'''|}}
-<!--Citation-->
 {{#if: {{#var: citation}}|==Citation==
-If you publish research that uses {{#var:app}} you have to cite it as follows:
+If you publish research that uses {{{app}}} you have to cite it as follows:
+WRITE CITATION HERE
-WRITE_CITATION_HERE
 |}}
-<!--Installation-->
-{{#if: {{#var: installation}}|==Installation==
-See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
-<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
-__NOTOC____NOEDITSECTION__