Difference between revisions of "PeakSplitter"
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Moskalenko (talk | contribs) (Created page with "=Usage= To load the PeakSplitter environment: $module load peaksplitter =Docs= To show the description: $module spider peaksplitter/1.0 '''After the peaksplitter module is lo…") |
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| − | + | __NOTOC__ | |
| − | + | __NOEDITSECTION__ | |
| − | + | [[Category:Software]][[Category:Bioinformatics]][[Category:NGS]] | |
| − | + | <!-- ######## 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|peaksplitter}} | ||
| + | |{{#vardefine:url|http://www.ebi.ac.uk/bertone/software.html}} | ||
| + | <!--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|}} <!--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--> | ||
| + | |{{#vardefine:policy|}} <!--Enable policy section --> | ||
| + | |{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | ||
| + | |{{#vardefine:faq|}} <!--Enable FAQ section --> | ||
| + | |{{#vardefine:citation|}} <!--Enable Reference/Citation section --> | ||
| + | |} | ||
| + | <!-- ######## Template Body ######## --> | ||
| + | <!--Description--> | ||
| + | {{#if: {{#var: url}}| | ||
| + | {{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | ||
| + | Subdivision of ChIP-seq/ChIP-chip regions into discrete signal peaks. | ||
| + | <!--Location--> | ||
| + | {{App_Location|app={{#var:app}}|{{#var:ver}}}} | ||
| + | ==Available Versions== | ||
| + | * 1.0 | ||
| + | {{#if: {{#var: mod}}|==Running the application using modules== | ||
| + | {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | ||
| + | {{#if: {{#var: exe}}|==How To Run== | ||
| + | |}} | ||
| + | {{#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== | ||
| + | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used) | ||
| + | |}} | ||
| + | {{#if: {{#var: testing}}|==Performance== | ||
| + | WRITE PERFORMANCE TESTING RESULTS HERE|}} | ||
| + | {{#if: {{#var: faq}}|==FAQ== | ||
| + | *'''Q:''' **'''A:''' | ||
| + | |}} | ||
| + | {{#if: {{#var: citation}}|==Citation== | ||
| + | If you publish research that uses {{#var: app}} you have to cite it as follows: | ||
| + | |}} | ||
Revision as of 20:33, 1 August 2012
Description
{{{name}}} website
Subdivision of ChIP-seq/ChIP-chip regions into discrete signal peaks.
Template:App Location
Available Versions
- 1.0
Running the application using modules
To use peaksplitter with the environment modules system at HPC the following commands are available:
Get module information for peaksplitter:
$module spider peaksplitter
Load the default application module:
$module load peaksplitter
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_PEAKSPLITTER_DIR - directory where peaksplitter is located.