Hoodini AMI example

This page records how the initial Hoodini environment was built on 16 July 2026. It used Ubuntu 26.04 LTS and commit a66a7d7 of the leightonpayne/hoodini fork.

Recorded build configuration

The build instance used the following settings:

Launch this short-lived builder in the research account. The instance type is only for the build process; the resulting AMI can run on compatible x86_64 instance types. Follow the general AMI preparation procedure and verify that the root volume is large enough before downloading the databases.

Installing Hoodini

Connect with Session Manager and install the prerequisites:

sudo apt-get update
sudo apt-get upgrade -y
sudo apt-get install -y \
    build-essential \
    zlib1g-dev \
    python3-dev

# Check the SSM Agent, should say enabled and active
sudo snap services amazon-ssm-agent

curl -fsSL https://pixi.sh/install.sh | bash
sudo ln -sf "$HOME/.pixi/bin/pixi" /usr/local/bin/pixi

Clone the pinned source and record the exact commit in the image:

cd /opt
sudo git clone https://github.com/leightonpayne/hoodini.git
cd hoodini
sudo git checkout a66a7d7
sudo git rev-parse HEAD | sudo tee /etc/hoodini-commit.txt

sudo pixi install
sudo pixi lock

The extra pixi lock was needed for the lock-file format at this recorded commit because it was complaining about outdated lock-file format version.

Download the data:

sudo pixi run hoodini download databases
sudo pixi run hoodini download metacerberus \
    amrfinder,cazy,cog,foam,gvdb,kegg,kofam,methmmdb,nfixdb,pfam,pgap,phrog,pvog,tigrfam,vog-r225

Install a wrapper so users can invoke Hoodini from any directory without Pixi updating the environment:

sudo tee /usr/local/bin/hoodini >/dev/null <<'EOF'
#!/usr/bin/env bash
set -euo pipefail
PROJECT=/opt/hoodini
exec pixi run \
    --as-is \
    --manifest-path "$PROJECT/pyproject.toml" \
    hoodini "$@"
EOF

sudo chmod 755 /usr/local/bin/hoodini

Run a small representative input to trigger downloading the assembly summaries:

cat > ~/test-input.txt <<'EOF'
WP_206356263.1
HFU9245413.1
WP_421098225.1
WP_247173889.1
WP_174771187.1
EOF

hoodini run \
    --input ~/test-input.txt \
    --output ~/test-output \
    --min-win 0 \
    --num-threads 8

Confirm that the run succeeds and inspect its output. Then remove test output, downloads, caches, credentials, and other build residue. Review paths before deleting them:

rm -rf ~/test-input.txt ~/test-output ~/.cache
sudo rm -rf /root/.ssh
sudo apt-get clean
history -c

Creating and testing the AMI

Create the AMI with these recorded details:

Wait until the AMI is available, then launch a test instance with the standard no-inbound security group and instance profile. Connect with Session Manager, confirm that /etc/hoodini-commit.txt contains a66a7d7, and repeat the small test.

Terminate both the test instance and the original builder after the image passes. Verify that their temporary EBS volumes were deleted.

Publishing the launch template

The initial supported template was recorded as:

Launch through the template itself and repeat the small test.