MagnetoGenie highlights R package not installed in conda environment

[seanmcallister]

Please see the error below. Looks like ggpubr isn't included in the R packages for the conda environment.

(magiclamp) sean-mini-server:2022_PCC_ManuscriptWork sean_server$ MagicLamp.py MagnetoGenie -bin_dir bins -bin_ext faa -out heme_MagnetoGenie -t 4 --orfs --makeplots
checking arguments
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.
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All required arguments provided!

starting main pipeline...
analyzing All_proteins_fullannotation_HEMEGENES.faa: 100%   
Identifying genomic proximities and putative operons
Clustering ORFs...

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Finished!
Running Rscript to generate plots. Do not be alarmed if you see Warning or Error messages from Rscript. This will not affect any of the output data that was already created. If you see plots generated, great! If not, you can plot the data as you wish on your own, or start an issue on MagnetoGenie's GitHub repository

Error in library("ggpubr", lib.loc = library.path) : 
  there is no package called ‘ggpubr’
Execution halted
Error in hclust(d = dist(x = fegenie.scaled)) : 
  must have n >= 2 objects to cluster
Calls: as.dendrogram -> hclust
Execution halted

...
Running Rscript to generate plots. Do not be alarmed if you see Warning or Error messages from Rscript. This will not affect any of the output data that was already created. If you see plots generated, great! If not, you can plot the data as you wish on your own, or start an issue on MagnetoGenie's GitHub repository

Error in library("ggpubr", lib.loc = library.path) : 
  there is no package called ‘ggpubr’
Execution halted
Error in hclust(d = dist(x = fegenie.scaled)) : 
  must have n >= 2 objects to cluster
Calls: as.dendrogram -> hclust
Execution halted

Results are written to heme_MagnetoGenie/magnetogenie-summary.csv and heme_MagnetoGenie/magnetogenie.heatmap.csv
Pipeline finished without crashing!!! Thanks for using :)

[Arkadiy-Garber]

I added ggpubr to the list of R packages installed with the setup.sh script.