Difference between revisions of "RiboPicker"
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==Installed Versions== | ==Installed Versions== | ||
* 0.4.2 | * 0.4.2 | ||
| + | * 0.4.3 (default) | ||
<!-- --> | <!-- --> | ||
{{#if: {{#var: mod}}|==Running the application using modules== | {{#if: {{#var: mod}}|==Running the application using modules== | ||
| Line 45: | Line 46: | ||
$module spider {{#var:app}} | $module spider {{#var:app}} | ||
{{#if: {{#var:intel}}|Load Intel compiler: {{#tag:pre|$module load intel/{{#var:intel}}}}|}}{{#if: {{#var:mpi}}|Load MPI implementation: {{#tag:pre|$module load {{#var:mpi}}}}|}} | {{#if: {{#var:intel}}|Load Intel compiler: {{#tag:pre|$module load intel/{{#var:intel}}}}|}}{{#if: {{#var:mpi}}|Load MPI implementation: {{#tag:pre|$module load {{#var:mpi}}}}|}} | ||
| − | |||
| − | |||
Load the application module: | Load the application module: | ||
$module load {{#var:app}} | $module load {{#var:app}} | ||
| Line 54: | Line 53: | ||
* HPC_{{uc:{{#var:app}}}}_DIR - directory where {{#var:app}} is located.|}} | * HPC_{{uc:{{#var:app}}}}_DIR - directory where {{#var:app}} is located.|}} | ||
* HPC_RIBOPICKER_BIN - executable 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 [http://edwards.sdsu.edu/ribopicker/rrnadb/ rrnadb]. | ||
| + | * 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== | {{#if: {{#var: exe}}|==How To Run== | ||
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
Revision as of 20:30, 11 January 2012
Description
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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.
Template:App Location
Installed Versions
- 0.4.2
- 0.4.3 (default)
Running the application using modules
To use ribopicker with the environment modules system at HPC the following commands are available:
Get module information for ribopicker:
$module spider ribopicker
Load the application module:
$module load ribopicker
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_RIBOPICKER_DIR - directory where ribopicker is located.
- 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