{% set name = "parascopy" %}
{% set version = "1.18.0" %}

package:
  name: {{ name|lower }}
  version: {{ version }}

build:
  number: 0
  entry_points:
    - parascopy = parascopy.entry_point:main
  run_exports:
    - {{ pin_subpackage('parascopy', max_pin="x") }}

source:
  url: https://github.com/tprodanov/{{ name }}/archive/v{{ version }}.tar.gz
  sha256: 29b3ddead7b079959bbdc058bf76b2951be906de7d3105bcfea67accc2c35a1f

requirements:
  build:
    - {{ compiler('c') }}
    - {{ compiler('cxx') }}
    - cmake
    - meson
    - ninja
    - pkg-config
  host:
    - python
    - pip
    - setuptools
    - bzip2
    - zlib
    - htslib
    - tabixpp
    - clangdev  # [osx]
    - liblzma
    - xz
  run:
    - python
    - numpy >=1.15
    - scipy >=1.5
    - pysam >=0.17
    - simpleeval >=0.9
    - parasail-python >=1.2
    - biopython >=1.70
    - samtools >=1.11
    - bwa >=0.7
    - intervaltree >=3.0
    - tabixpp
    - construct >=2.10

test:
  commands:
    - parascopy help
    - parascopy pretable --version
    - parascopy table --version
    - parascopy depth --version
    - parascopy cn --version
    - parascopy cn-using --version
    - parascopy pool --version
    - parascopy view --version
    - parascopy psvs --version
    - parascopy msa --version
    - parascopy call --version
    - _parascopy_freebayes --version

about:
  home: "https://github.com/tprodanov/parascopy"
  license: MIT
  license_family: MIT
  license_file: LICENSE
  summary: "Calling paralog-specific copy number and sequence variants in duplicated genes using short-read whole-genome sequencing."
  dev_url: "https://github.com/tprodanov/parascopy"
  doc_url: "https://github.com/tprodanov/parascopy/blob/v{{ version }}/README.md"

extra:
  additional-platforms:
    - linux-aarch64
    # ARM64 temporarily disabled as parasail is unable to detect m4
    #- osx-arm64
  identifiers:
    - doi:10.1038/s41467-022-30930-3
    - doi:10.1093/bioinformatics/btad268
    - biotools:parascopyvc
