Difference between revisions of "RGAugury"
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(Created page with "Category:SoftwareCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|RGAugury}} |{{#vardefine:url|https://bitbucket.org/yaanlpc/rgaugury}} <!--CO...") |
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| − | To run RGAugury, you should consider the following command | + | To run RGAugury, you should consider the following command usage as an example: |
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| + | <code>$ rgaugury </path/to/input_dir> -p <filename> -<other_arguments> </code> | ||
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| + | <code>$ RGAugury.pl </path/to/input_dir> -p <filename> -<other_arguments> </code> | ||
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<!--Job Scripts--> | <!--Job Scripts--> | ||
Latest revision as of 21:29, 30 November 2023
Description
A pipeline consisted of a couple of scripts for genome-wide RGAs prediction, most of single script in this package can work independently or together.
Environment Modules
Run module spider RGAugury to find out what environment modules are available for this application.
System Variables
- HPC_RGAUGURY_DIR - installation directory
- HPC_RGAUGURY_BIN - executable directory
- HPC_RGAUGURY_LIB - library directory
- SINGULARITYENV_PFAMDB - PFAM database directory inside the container
- SINGULARITYENV_PERL5LIB - Perl library directory inside the container
- SINGULARITYENV_PREPEND_PATH - pfam:interproscan directory inside the container
Additional Information
To run RGAugury, you should consider the following command usage as an example:
$ rgaugury </path/to/input_dir> -p <filename> -<other_arguments>
$ RGAugury.pl </path/to/input_dir> -p <filename> -<other_arguments>
Citation
If you publish research that uses RGAugury you have to cite it as follows:
Li, P., Quan, X., Jia, G., Xiao, J., Cloutier, S. and You, F.M. (2016) RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants. BMC genomics, 17, 852.