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This tutorial installs ViroSync, verifies its resources, and runs the shipped example. It requires Linux x86-64, Git, and Pixi.

Install ViroSync

git clone https://github.com/NeLLi-team/virosync.git
cd virosync
pixi install --locked

The lock file pins the software environment. Do not use Conda or the system Python for this project.

Install the core resources

pixi run setup-virosync-resources

For the first interactive install, select the core-resource location and confirm the download. For a non-interactive install, set VIROSYNC_DB_ROOT before setup.

This command downloads resources_v1_0_7_runtime.tar.gz, verifies its archive and manifest digests, and installs the read-only v1.0.7 resource tree under resources/virosync.

Run the full resource check:

pixi run virosync orchestrate resources verify \
  --config config/orchestration.yaml \
  --full

The output must include:

Version: v1.0.7
Authenticated payloads: 9

To store the resource tree outside the repository, set VIROSYNC_DB_ROOT before setup:

export VIROSYNC_DB_ROOT=/data/virosync-db
pixi run setup-virosync-resources

Keep the variable set for later runs.

Run the example

pixi run example

The task runs the genomes in example/ and writes to results/example/. Check the summary:

cat results/example/batch_summary.tsv

The test-1 row must have status=success, predictions=6, and accepted=1.

The task passes --clean-run, which ignores existing outputs and starts from scratch. To test resume, run the same input without that flag:

pixi run virosync \
  -i example/ \
  -o results/example \
  --config config/orchestration.yaml \
  -w 1 \
  --threads-per-worker 8

ViroSync reuses the completed genome only after it validates the run state and all recorded output files.

Run your genome

Point -i at a single FASTA file:

pixi run virosync \
  -i genome.fna \
  -o results/my_genome \
  --config config/orchestration.yaml \
  -w 1 \
  --threads-per-worker 16

Or at a directory of FASTA files:

pixi run virosync \
  -i genomes/ \
  -o results/my_genomes \
  --config config/orchestration.yaml \
  -w 4 \
  --threads-per-worker 16

ViroSync reads .fna, .fasta, and .fa files. It does not search subdirectories. -i also accepts a text file with one FASTA path per line. -w sets how many genomes run at the same time. --threads-per-worker sets the threads for each of those genomes.

See the command-line reference for run controls and methods and outputs for the result files.