package:
  name: lumpy-sv
  version: 0.3.0

source:
  url: https://github.com/arq5x/lumpy-sv/archive/0.3.0.tar.gz
  sha256: 8be9ce5010833021280d601e5bcb6baab3bc8be059e3524c1f4f664dee4c8e6d
  patches:
    - patch

build:
  number: 4
  skip: True  # [osx]

requirements:
  build:
    - {{ compiler('c') }}
    - {{ compiler('cxx') }}
    - cmake
  host:
    - htslib
    - sambamba #lumpy-express dependency
    - samblaster #lumpy-express dependency
    - samtools
  run:
    - htslib
    - python 2.7.*
    - samtools
    - gawk
    - pysam
    - numpy
    - util-linux #contains hexdump
    - sambamba #lumpy-express dependency
    - samblaster #lumpy-express dependency

test:
  commands:
    - 'lumpy 2>&1 | grep -q structural'
    - 'lumpy_filter 2>&1 | grep -q lumpy_filter\:\ usage'
    - 'lumpyexpress 2>&1 | grep -q lumpyexpress'
    - extractSplitReads_BwaMem --help

about:
  home: https://github.com/arq5x/lumpy-sv
  license: MIT
  summary: a general probabilistic framework for structural variant discovery
