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/...") |
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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_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_CONF - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
| Line 35: | Line 35: | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | Make sure to use | + | 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
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.