Difference between revisions of "RiboPicker"

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m (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==")
 
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__NOTOC__
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__NOTOC__ __NOEDITSECTION__
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[[Category:Software]][[Category:Biology]][[Category:Sequencing]]
[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
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{|<!--Main settings - REQUIRED-->
<!-- ########  Template Configuration ######## -->
 
<!--Edit definitions of the variables used in template calls
 
Required variables:
 
app - lowercase name of the application e.g. "amber"
 
url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
 
Optional variables:
 
INTEL - Version of the Intel Compiler e.g. "11.1"
 
MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
 
-->
 
{|
 
<!--Main settings - REQUIRED-->
 
 
|{{#vardefine:app|ribopicker}}
 
|{{#vardefine:app|ribopicker}}
 
|{{#vardefine:url|http://ribopicker.sourceforge.net/}}
 
|{{#vardefine:url|http://ribopicker.sourceforge.net/}}
<!--Compiler and MPI settings - OPTIONAL -->
 
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
<!--Choose sections to enable - OPTIONAL-->
 
|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
 
|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
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The riboPicker tool can be used to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.
 
The riboPicker tool can be used to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.
 
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<!--Modules-->
==Installed Versions==
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==Environment Modules==
* 0.4.2, 0.4.3 (EL5)
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* 0.4.3 (EL6)
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==System Variables==
<!-- -->
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
{{#if: {{#var: mod}}|==Execution Environment and Modules==
 
 
 
To use {{#var:app}} with the environment modules system at HPC the following commands are available:
 
 
 
Get module information for {{lc: {{PAGENAME}}}}:
 
$module spider {{#var:app}}
 
{{#if: {{#var:intel}}|Load Intel compiler: {{#tag:pre|$module load intel/{{#var:intel}}}}|}}{{#if: {{#var:mpi}}|Load MPI implementation: {{#tag:pre|$module load {{#var:mpi}}}}|}}
 
Load the application module:
 
$module load {{#var:app}}
 
 
 
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
 
 
 
* HPC_{{uc:{{#var:app}}}}_DIR - directory where {{#var:app}} is located.|}}
 
 
* HPC_RIBOPICKER_BIN - executable directory
 
* HPC_RIBOPICKER_BIN - executable directory
 
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<!--Additional-->
 +
{{#if: {{#var: exe}}|
 
==Databases==
 
==Databases==
 
The following Ribosomal RNA databases are available for use with RiboPicker at HPC:
 
The following Ribosomal RNA databases are available for use with RiboPicker at HPC:
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* ssr - Small Subunit RNA database from the SILVA project [http://www.arb-silva.de/no_cache/download/archive/release_108/Exports/ SSURef_108_NR_tax_silva_trunc_v2.fasta.tgz]
 
* ssr - Small Subunit RNA database from the SILVA project [http://www.arb-silva.de/no_cache/download/archive/release_108/Exports/ SSURef_108_NR_tax_silva_trunc_v2.fasta.tgz]
 
* lsr - Large Subunit non-redundant truncated database from the SILVA project [http://www.arb-silva.de/no_cache/download/archive/release_108/Exports/ LSURef_108_tax_silva_trunc.fasta.tgz]
 
* lsr - Large Subunit non-redundant truncated database from the SILVA project [http://www.arb-silva.de/no_cache/download/archive/release_108/Exports/ LSURef_108_tax_silva_trunc.fasta.tgz]
{{#if: {{#var: exe}}|==How To Run==
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A ''ribopicker'' alias was created for the main ribopicker.pl Perl script. To run RiboPicker use
 
A ''ribopicker'' alias was created for the main ribopicker.pl Perl script. To run RiboPicker use
 
  <code>ribopicker [options] -f &lt;file&gt; -dbs &lt;list&gt; ...</code>
 
  <code>ribopicker [options] -f &lt;file&gt; -dbs &lt;list&gt; ...</code>
 
For more information on the options run
 
For more information on the options run
 
  ribopicker -h
 
  ribopicker -h
|}}
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}}
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#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==
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: policy}}|==Usage policy==
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{{#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 (perhaps templates for a couple of main licensing schemes can be used)|}}
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==

Latest revision as of 21:50, 21 August 2022

Description

ribopicker website  

The riboPicker tool can be used to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.

Environment Modules

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

System Variables

  • HPC_RIBOPICKER_DIR - installation directory
  • HPC_RIBOPICKER_BIN - executable directory

Databases

The following Ribosomal RNA databases are available for use with RiboPicker at HPC:

A ribopicker alias was created for the main ribopicker.pl Perl script. To run RiboPicker use

ribopicker [options] -f <file> -dbs <list> ...

For more information on the options run

ribopicker -h