EMBOSS: Difference between revisions
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/ | [[Category:Software]][[Category:Bioinformatics]][[Category:NGS]] | ||
{|<!--CONFIGURATION: REQUIRED--> | |||
|{{#vardefine:app|emboss}} | |||
|{{#vardefine:url|http://emboss.sourceforge.net/}} | |||
<!--CONFIGURATION: OPTIONAL (1=ON)--> | |||
|{{#vardefine:mod|1}} <!--MODULES - NOW REQUIRED--> | |||
|{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice --> | |||
|{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice --> | |||
|{{#vardefine:exe|1}} <!--RUNNING --> | |||
|{{#vardefine:conf|}} <!--CONFIGS--> | |||
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |||
|{{#vardefine:policy|}} <!--POLICY--> | |||
|{{#vardefine:testing|}} <!--TESTING/PROFILING--> | |||
|{{#vardefine:faq|}} <!--FAQ--> | |||
|{{#vardefine:citation|}} <!--CITATION--> | |||
|{{#vardefine:installation|}} <!--INSTALLATION--> | |||
|} | |||
<!--BODY--> | |||
<!--Description--> | |||
{{#if: {{#var: url}}| | |||
{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | |||
EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages. | |||
<!--Location--> | |||
{{App_Location|app={{#var:app}}|{{#var:ver}}}} | |||
<!--Versions--> | |||
==Available versions== | |||
* 6.4.0 - EL5. | |||
* 6.5.7 - EL6. | |||
<!--Modules--> | |||
{{#if: {{#var: mod}}|==Running the application using modules== | |||
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | |||
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below--> | |||
<!--Run--> | |||
{{#if: {{#var: exe}}|==How To Run== | |||
EMBOSS is available both at the command line for use in the batch jobs and through the [[Galaxy]] Framework for Biocomputing. | |||
|}} | |||
<!--Configuration--> | |||
{{#if: {{#var: conf}}|==Configuration== | |||
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details. | |||
|}} | |||
<!--PBS scripts--> | |||
{{#if: {{#var: pbs}}|==PBS Script Examples== | |||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | |||
<!--Policy--> | |||
{{#if: {{#var: policy}}|==Usage policy== | |||
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used) | |||
|}} | |||
<!--Performance--> | |||
{{#if: {{#var: testing}}|==Performance== | |||
DOUBLE_CLICK_TO_WRITE_PERFORMANCE_TESTING_RESULTS_HERE | |||
|}} | |||
<!--Faq--> | |||
{{#if: {{#var: faq}}|==FAQ== | |||
*'''Q:''' **'''A:'''|}} | |||
<!--Citation--> | |||
{{#if: {{#var: citation}}|==Citation== | |||
If you publish research that uses {{#var:app}} you have to cite it as follows: | |||
DOUBLE_CLICK_TO_WRITE_CITATION_HERE | |||
|}} | |||
<!--Installation--> | |||
{{#if: {{#var: installation}}|==Installation== | |||
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | |||
__NOTOC____NOEDITSECTION__ | |||
Revision as of 16:23, 2 August 2012
Description
{{{name}}} website
EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.
Template:App Location
Available versions
- 6.4.0 - EL5.
- 6.5.7 - EL6.
Running the application using modules
To use emboss with the environment modules system at HPC the following commands are available:
Get module information for emboss:
$module spider emboss
Load the default application module:
$module load emboss
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_EMBOSS_DIR - directory where emboss is located.
How To Run
EMBOSS is available both at the command line for use in the batch jobs and through the Galaxy Framework for Biocomputing.