Difference between revisions of "RiboPicker"

Revision as of 19:42, 10 August 2012

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.

Required Modules

modules documentation

Serial

ribopicker

System Variables

HPC_{{#uppercase:ribopicker}}_DIR - installation directory
HPC_RIBOPICKER_BIN - executable directory

Additional Information

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 19: / Line 19: @@
 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.
+<!--Modules-->
-==Installed Versions==
+==Required Modules==
-* 0.4.2, 0.4.3 (EL5)
+[[Modules|modules documentation]]
-* 0.4.3 (EL6)
+===Serial===
-<!-- -->
+*{{#var:app}}
-{{#if: {{#var: mod}}|==Execution Environment and Modules==
+==System Variables==
+* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
-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
+<!--Additional-->
+{{#if: {{#var: exe}}|==Additional Information==
 ==Databases==
 The following Ribosomal RNA databases are available for use with RiboPicker at HPC:
@@ Line 44: / Line 34: @@
 * 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]
-{{#if: {{#var: exe}}|==How To Run==
 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>
 For more information on the options run
   ribopicker -h
-|}}
+}}
 {{#if: {{#var: conf}}|==Configuration==
 See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}