Docker is used for creating compute environments that exactly match where they were created. This aleviates a lot of the hassle of running code written by others.
Follow this link to install. If link is outdated, search "How to install docker"
This Docker image uses port 8181 to operate. If your port 8181 is in use, edit /docker-compose.yml:line18 to any available port (example, 8182)
If you are not running an Apple Silicon machine (M-series), see line 4-11 of /docker-compose.yml
Create a Docker image using the commands below. Installs dependencies with correct versions.
cd /path/to/this/directory
docker-compose up -d
This will download large amounts of data and might take a while.
Place your sequence file somewhere in this directory (ex: ./data/sample.fasta)
cd /path/to/this/directory
docker exec -it intactness bash
python3 -m intactness -in /app/data/sample.fasta
Point the -in flag to your sequence file.
Result summary will be found at -in/intactness/summary.csv
Genome diagrams will be found at -in/intactness/Alignment_Views/*
Note: /app is the working directory for this Docker environment. It links and updates this code on your computer to that location.
Ensure your Docker client is running.