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}}}}|}} | ||
| + | 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.