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#create an interactive session
qsub -I -S /bin/bash -l walltime=10:00:00 -l select=1:ncpus=2:mem=4gb

#create conda environment
conda create --name nanoQ2 python=3.7
conda activate nanoQ2

#install tools
conda install -c bioconda pysam
conda install -c conda-forge numpy
conda install -c conda-forge scipy
conda install -c conda-forge matplotlib
conda install -c conda-forge biopython

#aligners
conda install -c bioconda minimap2
conda install -c bioconda graphmap

#fetch nano-Q
git clone https://github.com/PrestonLeung/Nano-Q.git

#change directory to Nano-Q
cd Nano-Q

#make all python scripts executable
chmod +x *.py

#copy all python scripts to your /home/bin/

cp *.py ~/bin