:'Copyright <2021> #Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"),\ to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,\ and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.\ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE\ OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ' #!/bin/bash # Moves into the working directory cd /path/to/working/directory #Defines the input and output path variables Input_path='/path/to/input/files' Output_path='/path/to/output/directory' #Loads the Anaconda module module load Anaconda/2020.07 #Activates the conda environment where PIRATE is installed source activate pirate_env #Runs PIRATE with the -a -r -t options which align the genomes and prints summary figures using 12 threads PIRATE -i $Input_path -s "50,70,90,95,98" -o $Output_path -a -r -t 12 #Deactivates the conda environment conda deactivate #prints a message that the script executed successfully echo "It worked"