Insallation of pipeline dependencies uses conda and homebrew, and requires macOS or Linux (no Windows support).
Package managers
Install conda
Install homebrew
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
Enter the following command into your terminal to install all dependencies:
wget -O - https://raw.githubusercontent.com/iframst/HybridAMRgenotyping/main/Manual/deps_install.sh | bash
Alternatively, install pipeline dependencies from their respective sources.
- Porechop
- flye
- canu
- unicycler
- BWA
- samtools
- QUAST
- Prokka
- AMR finder
- spades
- minimap2
- pilon
- racon
- metaphlan2
Next: Usage