Setup and Usage

This page is a quickstart for first-time users. It summarizes setup and links to authoritative resource references.

Help menus

Use help menus at each level:

pyfuse --help
pyfuse annotator --help
pyfuse resources --help
pyfuse resources install --help

Install package

python -m venv .venv
source .venv/bin/activate
pip install --upgrade git+https://github.com/gopisiva1616/PyFuse.git

Note: PyPI and Conda packages are not yet available. See the project documentation for updated package-manager install commands when they are published.

Resource setup is required

PyFuse annotator requires an installed resource bundle. Setup is genome-specific.

Typical install time:

  • Resource building can take around 30 minutes to 1 hour depending on selected genome and options.
  • PyFuse reports total elapsed time at the end of both resources and annotator runs.

You should install at least once for each genome build you plan to run:

pyfuse resources install --genome grch37
pyfuse resources install --genome grch38

If you only work in one genome build, install only that build.

Resource commands you should know

pyfuse resources list
pyfuse resources verify --genome grch37
pyfuse resources path --genome grch38
  • list: shows installed versions per genome
  • verify: checks manifest/files for latest version of that genome
  • path: prints the exact latest bundle path selected for that genome

How annotator picks resources

Default behavior:

  1. PyFuse selects latest installed bundle for --genome.
  2. If no bundle exists for that genome, PyFuse exits with install guidance.

Override behavior:

  1. If --resource_path is provided, that exact bundle is used for that run.

Examples:

pyfuse annotator -i path/to/fusions.tsv -o output_dir --input_format star --genome grch37
pyfuse annotator -i path/to/fusions.tsv -o output_dir --input_format arriba --resource_path path/to/custom_bundle

Resource root and settings overrides

Resource root precedence for resources commands (install/list/path/verify):

  1. --resource-root
  2. PYFUSE_RESOURCE_ROOT environment variable
  3. resource_root in settings file
  4. platform default user data directory

Settings file behavior:

  • pass a settings file with -s/--settings
  • settings can define resource_root and default install inputs (default_refseq_gtf_url_grch37, default_refseq_gtf_url_grch38, default_refseq_assembly_summary_url_grch37, default_refseq_assembly_summary_url_grch38, default_mane_url)
  • explicit CLI flags override settings values for that run

Example:

pyfuse -s /path/custom_settings.yaml resources install --genome grch38
pyfuse -s /path/custom_settings.yaml resources install --genome grch38 --gtf /data/custom.gtf.gz