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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
conda install -c bioconda samtools
#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 |
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