Difference between revisions of "EMBOSS"
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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}}|name={{#var:app}}}}|}} | ||
| − | + | 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. | |
| + | <!--Modules--> | ||
| + | ==Environment Modules== | ||
| + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
| + | ==System Variables== | ||
| + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| + | <!--Additional--> | ||
| + | {{#if: {{#var: exe}}|==Additional Information== | ||
| + | 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 18:25, 10 June 2022
Description
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.