{% set version = "1.6.1" %}

package:
  name: bactopia
  version: {{ version }}

build:
  number: 0
  noarch: generic

source:
  url: https://github.com/bactopia/bactopia/archive/v{{version}}.tar.gz
  sha256: b683fa69852873621b440673a58df459939ef5b386a21db519971f28b279b62d

requirements:
  run:
    - ariba
    - beautifulsoup4
    - biopython
    - blast >=2.10.1
    - bowtie2 <2.4.0 
    - cd-hit
    - conda
    - coreutils
    - executor
    - lxml
    - mash
    - ncbi-amrfinderplus
    - ncbi-genome-download
    - nextflow
    - pysam >=0.15.3 # older versions have wrong openssl pinning
    - python >3.6
    - requests 
    - sed
    - unzip
    - wget

test:
  commands:
    - "bactopia --conda_help"
    - "bactopia --version"
    - "bactopia datasets --help"
    - "bactopia prepare"
    - "bactopia search"
    - "bactopia tools"

about:
  home: https://bactopia.github.io/
  license: MIT
  license_file: LICENSE
  summary: Bactopia is a flexible pipeline for complete analysis of bacterial genomes.
  dev_url: https://github.com/bactopia/bactopia/

extra:
  recipe-maintainers:
    - rpetit3
  identifiers:
    - biotools:bactopia
    - doi:10.1128/mSystems.00190-20
