Difference between revisions of "RiboPicker"

Latest revision as of 21:50, 21 August 2022

Description

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:

rrnadb - Non-redundant Ribosomal RNA database from rrnadb.
ssr - Small Subunit RNA database from the SILVA project SSURef_108_NR_tax_silva_trunc_v2.fasta.tgz
lsr - Large Subunit non-redundant truncated database from the SILVA project LSURef_108_tax_silva_trunc.fasta.tgz

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

@@ Line 1: / Line 1: @@
-__NOTOC__
+__NOTOC__ __NOEDITSECTION__
-__NOEDITSECTION__
+[[Category:Software]][[Category:Biology]][[Category:Sequencing]]
-[[Category:Software]]
+{|<!--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:url|http://ribopicker.sourceforge.net/}}
-<!--Compiler and MPI settings - OPTIONAL -->
+|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
-|{{#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|}} <!--Present manual instructions for running the software -->
 |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
@@ Line 31: / Line 15: @@
 <!--Description-->
 {{#if: {{#var: url}}|
-{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
+{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 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.
-<!--Location-->
+<!--Modules-->
-{{App_Location|app={{#var:app}}|{{#var:ver}}}}
+==Environment Modules==
-==Installed Versions==
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-* 0.4.2
+==System Variables==
-<!-- -->
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-{{#if: {{#var: mod}}|==Running the application using modules==
+* HPC_RIBOPICKER_BIN - executable directory
+<!--Additional-->
-To use {{#var:app}} with the environment modules system at HPC the following commands are available:
+{{#if: {{#var: exe}}|
+==Databases==
-Get module information for {{lc: {{PAGENAME}}}}:
+The following Ribosomal RNA databases are available for use with RiboPicker at HPC:
- $module spider {{#var:app}}
+* rrnadb - Non-redundant Ribosomal RNA database from [http://edwards.sdsu.edu/ribopicker/rrnadb/ rrnadb].
-{{#if: {{#var:intel}}|Load Intel compiler: {{#tag:pre|$module load intel/{{#var:intel}}}}|}}{{#if: {{#var:mpi}}|Load MPI implementation: {{#tag:pre|$module load {{#var:mpi}}}}|}}
+* 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]
-Load the application module:
+* 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]
- $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:
+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>
-* HPC_{{uc:{{#var:app}}}}_DIR - directory where {{#var:app}} is located.|}}
+For more information on the options run
-* HPC_RIBOPICKER_BIN - executable directory
+ ribopicker -h
-'''ribopicker module depends on the perl module, so module load perl first.'''
+}}
-{{#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.|}}
 {{#if: {{#var: pbs}}|==PBS Script Examples==
 See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
-{{#if: {{#var: policy}}|==Usage policy==
+{{#if: {{#var: policy}}|==Usage Policy==
 WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 {{#if: {{#var: testing}}|==Performance==