{% set version = "5.0.2" %}
{% set hash = "2b31aac010f5c04d5367f1bf718516ae" %}

package:
  name: quast
  version: {{ version }}

build:
  number: 5
  # Needs to adjust cgi.escape to be html.escape for Python 3.8.
  # (cgi.escape is deprecated since 3.2)
  # AttributeError: module 'cgi' has no attribute 'escape'
  skip: True  # [py>=38]

source:
  url:
    - https://github.com/ablab/quast/releases/download/quast_{{ version }}/quast-{{ version }}.tar.gz
    - http://downloads.sourceforge.net/project/quast/quast-{{ version }}.tar.gz
  md5: {{ hash }}
  patches:
    - genemark-issue_disable-and-exclude-from-package.patch
    - skip-glimmer-in-test.patch
    - remove-explicit-dependencies-from-setup-py.patch

requirements:
  build:
    - {{ compiler('c') }}    
    - {{ compiler('cxx') }}
    - make
  host:
    - perl
    - python
    - pip
    - setuptools
    - matplotlib-base
    - joblib
    - simplejson
    - blast
    - zlib
    - glimmerHMM
    - circos
    - minimap2 >=2.10
  run:
    - perl
    - python
    - matplotlib-base
    - openjdk >=8
    - joblib
    - simplejson
    - blast
    - zlib
    - glimmerHMM
    - circos
    - minimap2 >=2.10

test:
  source_files:
    - test_data
  commands:
    - quast --version
    - metaquast --version

about:
  home: http://quast.sourceforge.net/
  license: Custom
  license_file: LICENSE.txt
  summary: Quality Assessment Tool for Genome Assemblies

extra:
  container:
    # ascii fallback fails without locale
    extended-base: true
  notes: |
    - GeneMark gene prediction software is disabled due to licensing issues
  identifiers:
    - biotools:quast
    - doi:10.1093/bioinformatics/btt086
