{% set version = "1.5.2" %}

package:
  name: abyss
  version: {{ version }}

build:
  number: 6

source:
  url: https://github.com/bcgsc/abyss/releases/download/{{ version }}/abyss-{{ version }}.tar.gz
  md5: 10d6d72d1a915e618d41a5cbbcf2364c
  patches:
    - osx-std_string_length-no-export.patch  # can be removed for "abyss >2.0.2"

requirements:
  build:
    - {{ compiler('cxx') }}
  host:
    - boost
    - sparsehash
    - sqlite
    - openmpi

  run:
    - bwa
    - sqlite
    - make
    - openmpi

test:
  commands:
    - ABYSS-P --version | grep -q "{{ version }}"
    - ABYSS --version | grep -q "{{ version }}"
    - abyss-pe help | grep -q "Assemble reads into contigs and scaffolds"

about:
  home: http://www.bcgsc.ca/platform/bioinfo/software/abyss
  license: GPL3
  license_file: LICENSE
  summary: Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

extra:
  container:
    # openmpi needs ssh/rsh
    extended-base: true
  identifiers:
    - biotools:abyss
    - doi:10.1101/gr.089532.108
