1. You need to install some python packages(include biopython,pyspark and numpy) which can be installed by Python's package manager pip. Here are simplest way to install pacakges:

pip install biopython  

pip install numpy   

pip install pyspark  

If you can't install packages successfully,please google it.

2. now you can move all these files(include SW_align.py,SWSpark.py,query.file, db.file,Smith_Waterman_spark.sh) to your spark direcotory.

3. move the config file to conf/ directory:

 mv spark-env.sh path/to/your/spark/conf/

4. Run the below command:

cd path/to/your/spark/directory  

sh Smith_Waterman_spark.sh  

for my machine,it is:

cd /home/cyw/spark-2.3.1-bin-hadoop2.7/  

sh Smith_Waterman_spark.sh  

5. the result will be write to files in directory aligned.csv/

6. If you want to run the single machine version Smith-waterman,please run :

python SW_align.py  

Result will be write to 'single_machine.txt'.