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.
module spider RGAugury to find out what environment modules are available for this application.
- 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
To run RGAugury, you should consider the following command format as an example:
$ rgaugury </path/to/input_dir> -p <filename> -<other_arguments>
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.