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2. Installation
ALPPACA is a Nextflow pipeline, and allows for flexible execution. Before installing the pipeline, make sure you have the following dependencies installed on your target system:
- Nextflow >= 21.10.6
- Java >= 7.0.91
Feel free to create a conda environment with the necessary dependencies using the assets/env.yml file in the main repository.
Then, you may install the pipeline by cloning the GitHub repository:
git clone [email protected]:NorwegianVeterinaryInstitute/ALPPACA.git
The pipeline may also be executed directly from GitHub without downloading the pipeline:
nextflow run NorwegianVeterinaryInstitute/ALPPACA <params>
For the core_gene track, you need a reference mash database. This can be downloaded here.
The pipeline provides a test functionality. The test will run the core_genome track of the pipeline, and will automatically download the necessary files needed for the test run.
If you have already cloned the repository to your system, use the following to run the test:
nextflow run /path/to/ALPPACA/main.nf -profile test_core_genome,<docker/singularity/conda> --out_dir <dirname>
The test can also be run directly from GitHub:
nextflow run NorwegianVeterinaryInstitute/ALPPACA -profile test_core_genome,<docker/singularity/conda> --out_dir <dirname>
A directory with the provided dirname will be generated in the directory you run the pipeline from, which holds the results from the pipeline.