https://help.rc.ufl.edu/mediawiki/index.php?title=MGERT&feed=atom&action=history
MGERT - Revision history
2024-03-29T07:59:17Z
Revision history for this page on the wiki
MediaWiki 1.35.13
https://help.rc.ufl.edu/mediawiki/index.php?title=MGERT&diff=20588&oldid=prev
Maxprok at 14:20, 15 September 2020
2020-09-15T14:20:47Z
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 14:20, 15 September 2020</td>
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Maxprok
https://help.rc.ufl.edu/mediawiki/index.php?title=MGERT&diff=20587&oldid=prev
Maxprok: Created page with "Category:SoftwareCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|mgert}} |{{#vardefine:url|https://github.com/andrewgull/MGERT}} <!--CONFIGUR..."
2020-09-15T14:20:39Z
<p>Created page with "<a href="/doc/Category:Software" title="Category:Software">Category:Software</a><a href="/doc/Category:Phylogenetics" title="Category:Phylogenetics">Category:Phylogenetics</a> {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|mgert}} |{{#vardefine:url|https://github.com/andrewgull/MGERT}} <!--CONFIGUR..."</p>
<p><b>New page</b></p><div>[[Category:Software]][[Category:Phylogenetics]]<br />
{|<!--CONFIGURATION: REQUIRED--><br />
|{{#vardefine:app|mgert}}<br />
|{{#vardefine:url|https://github.com/andrewgull/MGERT}}<br />
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--><br />
|{{#vardefine:conf|}} <!--CONFIGURATION--><br />
|{{#vardefine:exe|}} <!--ADDITIONAL INFO--><br />
|{{#vardefine:job|}} <!--JOB SCRIPTS--><br />
|{{#vardefine:policy|}} <!--POLICY--><br />
|{{#vardefine:testing|}} <!--PROFILING--><br />
|{{#vardefine:faq|}} <!--FAQ--><br />
|{{#vardefine:citation|}} <!--CITATION--><br />
|{{#vardefine:installation|}} <!--INSTALLATION--><br />
|}<br />
<!--BODY--><br />
<!--Description--><br />
{{#if: {{#var: url}}|<br />
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}<br />
<br />
MGERT is a computational pipeline for easy retrieving of MGE's coding sequences of a particular family from genome assemblies. MGERT utilizes several established bioinformatic tools combined into single pipeline which hides different technical quirks from an inexperienced user.<br />
<br />
<!--Modules--><br />
==Environment Modules==<br />
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.<br />
==System Variables==<br />
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory<br />
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory<br />
<br />
<!--Configuration--><br />
{{#if: {{#var: conf}}|==Configuration==<br />
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.<br />
|}}<br />
<!--Run--><br />
{{#if: {{#var: exe}}|==Additional Information==<br />
<br />
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY<br />
<br />
|}}<br />
<!--Job Scripts--><br />
{{#if: {{#var: job}}|==Job Script Examples==<br />
See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.<br />
|}}<br />
<!--Policy--><br />
{{#if: {{#var: policy}}|==Usage Policy==<br />
<br />
WRITE USAGE POLICY HERE (Licensing, usage, access).<br />
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|}}<br />
<!--Performance--><br />
{{#if: {{#var: testing}}|==Performance==<br />
<br />
WRITE_PERFORMANCE_TESTING_RESULTS_HERE<br />
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|}}<br />
<!--Faq--><br />
{{#if: {{#var: faq}}|==FAQ==<br />
*'''Q:''' **'''A:'''|}}<br />
<!--Citation--><br />
{{#if: {{#var: citation}}|==Citation==<br />
If you publish research that uses {{#var:app}} you have to cite it as follows:<br />
<br />
[https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-019-0163-6 Guliaev AS, Semyenova SK. MGERT: a pipeline to retrieve coding sequences of mobile genetic elements from genome assemblies. Mob DNA. 2019;10(1):21. doi:10.1186/s13100-019-0163-6]<br />
<br />
|}}<br />
<!--Installation--><br />
{{#if: {{#var: installation}}|==Installation==<br />
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}<br />
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Maxprok