{% set version = "1.52.0" %}
{% set name = "deepSNV" %}
{% set bioc = "3.20" %}

about:
  description: This package provides provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The deepSNV algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs. The shearwater algorithm computes a Bayes classifier based on a beta-binomial model for variant calling with multiple samples for precisely estimating model parameters - such as local error rates and dispersion - and prior knowledge, e.g. from variation data bases such as COSMIC.
  home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html
  license: GPL-3
  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
  summary: Detection of subclonal SNVs in deep sequencing data.

build:
  number: 1
  rpaths:
    - lib/R/lib/
    - lib/
  run_exports: '{{ pin_subpackage("bioconductor-deepsnv", max_pin="x.x") }}'

extra:
  additional-platforms:
    - linux-aarch64

  identifiers:
    - biotools:deepsnv
  parent_recipe:
    name: bioconductor-deepsnv
    path: recipes/bioconductor-deepsnv
    version: 1.26.1

package:
  name: bioconductor-{{ name|lower }}
  version: '{{ version }}'

# Suggests: RColorBrewer, knitr, rmarkdown
# SystemRequirements: GNU make
requirements:
  build:
    - {{ compiler('c') }}
    - {{ compiler('cxx') }}
    - make
  host:
    - bioconductor-biostrings >=2.74.0,<2.75.0
    - bioconductor-genomicranges >=1.58.0,<1.59.0
    - bioconductor-iranges >=2.40.0,<2.41.0
    - bioconductor-rhtslib >=3.2.0,<3.3.0
    - bioconductor-summarizedexperiment >=1.36.0,<1.37.0
    - bioconductor-variantannotation >=1.52.0,<1.53.0
    - r-base
    - r-vgam
    - libblas
    - liblapack
    - zlib
    - liblzma-devel
  run:
    - bioconductor-biostrings >=2.74.0,<2.75.0
    - bioconductor-genomicranges >=1.58.0,<1.59.0
    - bioconductor-iranges >=2.40.0,<2.41.0
    - bioconductor-rhtslib >=3.2.0,<3.3.0
    - bioconductor-summarizedexperiment >=1.36.0,<1.37.0
    - bioconductor-variantannotation >=1.52.0,<1.53.0
    - r-base
    - r-vgam

source:
  md5: 23f4830f8b5ad3b1c38ef91ad6427a9a
  url:
    - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz
    - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz
    - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz
    - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz

test:
  commands:
    - $R -e "library('{{ name }}')"

