Difference between revisions of "Necklace"

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(Created page with "Category:SoftwareCategory:BiologyCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|necklace}} |{{#vardefine:url|https://github.com/Oshlack/...")
 
m (Text replacement - "#uppercase" to "uc")
 
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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_{{#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}}}}_CONF - installation directory
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* HPC_{{uc:{{#var:app}}}}_CONF - installation directory
  
 
<!--Configuration-->
 
<!--Configuration-->
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{{#if: {{#var: exe}}|==Additional Information==
 
{{#if: {{#var: exe}}|==Additional Information==
  
Make sure to use * HPC_{{#uppercase:{{#var:app}}}}_CONF to point the software to the necklace.groovy file.
+
Make sure to use HPC_{{uc:{{#var:app}}}}_CONF to point the software to the necklace.groovy file.
  
 
|}}
 
|}}

Latest revision as of 21:22, 6 December 2019

Description

necklace website  

In species where the reference genome or annotation is incomplete, RNA-Seq analyses can benefit from performing a genome-guided and de novo assembly, in addition to using the reference annotation. Necklace is a software pipeline to run genome-guided and de novo assembly and combine the resulting transcriptomes with reference genome annotations. Necklace constructs a compact but comprehensive superTranscriptome

Environment Modules

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

System Variables

  • HPC_NECKLACE_DIR - installation directory
  • HPC_NECKLACE_BIN - executable directory
  • HPC_NECKLACE_CONF - installation directory


Additional Information

Make sure to use HPC_NECKLACE_CONF to point the software to the necklace.groovy file.