Resource Install Options and Examples

Use pyfuse resources install to build/install a managed bundle.

Start with help menus:

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

Operational Notes

  • Resource building can take about 30 minutes to 1 hour depending on genome, network speed, and override options.

Command shape

pyfuse resources install --genome {grch37|grch38} [options]

Option Summary

  • --genome: required genome build
  • --source: refseq-gtf (default) or ucsc-gtf
  • --gtf: optional GTF input override (<url_or_file>)
  • --annot-summary: optional assembly summary override (<url_or_file>)
  • --mane-file: optional MANE override (<url_or_file>)
  • --cache-dir: optional cache location for staging/downloads
  • --resource-root: optional managed resource root

Top-level option shared by all subcommands:

  • -s, --settings: optional custom settings YAML

Input files and formats

For installer inputs (--gtf, --annot-summary, --mane-file), accepted forms are:

  • URL (downloaded and staged)
  • local file path (used directly)

Runtime order: During runtime, inputs are chosen in the following order until corresponding values are found:

  1. explicit CLI option
  2. value from custom settings passed with -s/--settings
  3. packaged defaults from src/pyfuse/config/settings.yaml

Per-Option Behavior

--gtf

Default behavior: Uses genome-specific RefSeq GTF URL in packaged settings.

Override methods:

  • CLI: --gtf <url_or_file> or

  • Custom settings YAML: set "default_refseq_gtf_url_grch37" and "default_refseq_gtf_url_grch38" in a file passed with -s/--settings

--annot-summary

Default behavior: Uses genome-specific RefSeq assembly summary URL in packaged settings.

Override methods: - CLI: --annot-summary <url_or_file> - Custom settings YAML: set "default_refseq_assembly_summary_url_grch37" and "default_refseq_assembly_summary_url_grch38" in a file passed with -s/--settings

--mane-file

Default behavior: Uses "default_mane_url" in packaged settings.

  • Default value: NCBI MANE current directory
  • MANE directory URL resolves to latest summary file automatically.
  • Direct summary URL ending with .summary.txt.gz is also accepted.
  • For default GRCh37 setup, MANE is skipped.

Override methods: - CLI: --mane-file <url_or_file> - Custom settings YAML: set "default_mane_url" in a file passed with -s/--settings

GRCh37 note: - If a non-default MANE input is provided, PyFuse warns and asks for explicit confirmation.

Compatibility alias accepted by CLI: --mane-url.

Run help to view exact defaults:

pyfuse resources install -h

Examples

Default GRCh37 install

pyfuse resources install --genome grch37

Default GRCh38 install

pyfuse resources install --genome grch38

List what is installed

pyfuse resources list

Verify latest installed bundle for a genome

pyfuse resources verify --genome grch37
pyfuse resources verify --genome grch38

pyfuse resources path --genome grch37
pyfuse resources path --genome grch38

Override with custom local files

pyfuse resources install --genome grch38 \
  --gtf /data/ref/GRCh38_latest_genomic.gtf.gz \
  --annot-summary /data/ref/GRCh38_latest_assembly_report.txt

Install and store managed bundles under a custom root

pyfuse resources install --genome grch38 --resource-root /data/pyfuse_resources

Use a settings file, then override one value from CLI

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

Override with custom URLs

pyfuse resources install --genome grch38 \
  --gtf https://example.org/custom.gtf.gz \
  --annot-summary https://example.org/custom_assembly_report.txt

GRCh37 with explicit back-mapped MANE URL

pyfuse resources install --genome grch37 --mane-file https://example.org/backmapped_mane/

PyFuse will warn and ask for explicit confirmation before using MANE for GRCh37.

Resource Root Precedence

For resources subcommands (install, list, path, verify):

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