Revision as of 18:04, 27 May 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.

Required Modules

modules documentation

Serial

mira

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.

Validation

Validated 4/5/2018

@@ 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==
+==Required Modules==
-Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
+[[Modules|modules documentation]]
+===Serial===
+*{{#var:app}}
 ==System Variables==
 * HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 * HPC_{{uc:{{#var:app}}}}_BIN - executable 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-->
+=Validation=
-{{#if: {{#var: installation}}|==Installation==
+* Validated 4/5/2018
-See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
-<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
-__NOTOC____NOEDITSECTION__

Difference between revisions of "MIRA"