# Notes for Adesola ## Using rMAP on ARC4 After installing the conda environment we need to activate the environment to enter into it so we can use the installed software. ```bash= $ source activate rMAP-1.0 (rMAP-1.0) $ ``` ### Creating a directory ```bash= $ mkdir exp_inputs # to move all the fastq files to the exp_inputs folder $ mv Sal01_S39_*.fastq* exp_inputs ``` ### Next steps Log back onto ARC4, run all this from your home directory. ```bash= $ source activate rMAP-1.0 # install dependencies (rMAP-1.0) $ rMAP/bin/rMAP -t 8 -c # to do a test run (rMAP-1.0) $ rMAP/bin/rMAP -t 8 --reference salreference.gb \ --input testsal --output salresult \ --quality --assembly shovill --amr \ --varcall --trim --phylogeny --pangenome --gen-ele ```