- install via [pip](https://pypi.org/project/squigualiser/)
python3.8 -m venv venv3
source venv3/bin/activate
pip install --upgrade pip
pip install squigualiser
- Or use the pre-compiled binary release for common Linux distributions
wget https://github.com/hiruna72/squigualiser/releases/download/v0.3.0/squigualiser-v0.3.0-linux-x86-64-binaries.tar.gz -O squigualiser.tar.gz
tar xf squigualiser.tar.gz
cd squigualiser
./squigualiser --help
- Or use the pre-compiled binary release for common macOS distributions
wget https://github.com/hiruna72/squigualiser/releases/download/v0.3.0/squigualiser-v0.3.0-macos-arm64-binaries.tar.gz -O squigualiser.tar.gz
or use curl
curl -L https://github.com/hiruna72/squigualiser/releases/download/v0.3.0/squigualiser-v0.3.0-macos-arm64-binaries.tar.gz -O squigualiser.tar.gz
tar xf squigualiser.tar.gz
cd squigualiser
./squigualiser --help
- For a quick test run the following
`
wget https://github.com/hiruna72/squigualiser/releases/download/v0.3.0/sample_dataset.tar.gz
or use curl
curl -L https://github.com/hiruna72/squigualiser/releases/download/v0.3.0/sample_dataset.tar.gz -o sample_dataset.tar.gz
tar xf sample_dataset.tar.gz
./squigualiser plot_pileup -f ref.fasta -s reads.blow5 -a eventalign.bam -o dir_out --region chr1:92,778,040-92,782,120 --tag_name "test_0"
`
- `export PATH=[path_to_squigualiser_dir]:$PATH` to execute `squigualiser` from any location.