Difference between revisions of "EMBOSS"

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(Created page with "/apps/emboss/6.4.0/ Be sure to set PLPLOT_LIB=/apps/emboss/6.4.0/lib")
 
 
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/apps/emboss/6.4.0/
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[[Category:Software]][[Category:Biology]]
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{|<!--CONFIGURATION: REQUIRED-->
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|{{#vardefine:app|emboss}}
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|{{#vardefine:url|http://emboss.sourceforge.net/}}
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<!--CONFIGURATION: OPTIONAL (1=ON)-->
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|{{#vardefine:mod|1}} <!--MODULES - NOW REQUIRED-->
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|{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice -->
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|{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice -->
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|{{#vardefine:exe|1}} <!--RUNNING -->
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|{{#vardefine:conf|}} <!--CONFIGS-->
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|{{#vardefine:pbs|}} <!--PBS SCRIPTS-->
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|{{#vardefine:policy|}} <!--POLICY-->
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|{{#vardefine:testing|}} <!--TESTING/PROFILING-->
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|{{#vardefine:faq|}} <!--FAQ-->
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|{{#vardefine:citation|}} <!--CITATION-->
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|{{#vardefine:installation|}} <!--INSTALLATION-->
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|}
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<!--BODY-->
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<!--Description-->
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{{#if: {{#var: url}}|
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
  
Be sure to set PLPLOT_LIB=/apps/emboss/6.4.0/lib
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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.
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<!--Modules-->
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==Environment Modules==
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
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==System Variables==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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<!--Additional-->
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{{#if: {{#var: exe}}|==Additional Information==
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EMBOSS is available both at the command line for use in the batch jobs and through the [[Galaxy]] Framework for Biocomputing.
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|}}
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<!--Configuration-->
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{{#if: {{#var: conf}}|==Configuration==
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See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
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|}}
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<!--PBS scripts-->
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{{#if: {{#var: pbs}}|==PBS Script Examples==
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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
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<!--Policy-->
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{{#if: {{#var: policy}}|==Usage Policy==
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WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)
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|}}
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<!--Performance-->
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{{#if: {{#var: testing}}|==Performance==
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DOUBLE_CLICK_TO_WRITE_PERFORMANCE_TESTING_RESULTS_HERE
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|}}
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<!--Faq-->
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{{#if: {{#var: faq}}|==FAQ==
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*'''Q:''' **'''A:'''|}}
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<!--Citation-->
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{{#if: {{#var: citation}}|==Citation==
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If you publish research that uses {{#var:app}} you have to cite it as follows:
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DOUBLE_CLICK_TO_WRITE_CITATION_HERE
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|}}
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<!--Installation-->
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{{#if: {{#var: installation}}|==Installation==
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See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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__NOTOC____NOEDITSECTION__

Latest revision as of 15:01, 15 August 2022

Description

emboss 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.

Environment Modules

Run module spider emboss to find out what environment modules are available for this application.

System Variables

  • HPC_EMBOSS_DIR - installation directory

Additional Information

EMBOSS is available both at the command line for use in the batch jobs and through the Galaxy Framework for Biocomputing.