package:
  name: bowtie2
  version: 2.2.1

source:
  url: https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.1/bowtie2-2.2.1-source.zip
  sha256: 32728b127abf0a8c3aa48e6fb8bf81a9133f54da7e065c2a7bd3410704195f9d

build:
  number: 2
  skip: True  # [osx]

requirements:
  build:
    - {{ compiler('cxx') }}
  host:
    - python
  run:
    - python
    - perl

test:
  commands:
    - bowtie2 --version
    - bowtie2-build --help
    - bowtie2-inspect-l --help
    - bowtie2-align-s --help
    - bowtie2_wrapper.sh -h

about:
  home: 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
  license: GPLv3
  summary: 'Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing
    reads to long reference sequences. It is particularly good at aligning reads of
    about 50 up to 100s or 1,000s of characters, and particularly good at aligning
    to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with
    an FM Index to keep its memory footprint small: for the human genome, its memory
    footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end
    alignment modes.   http://bowtie-bio.sourceforge.net/bowtie2/index.shtml '

extra:
  identifiers:
    - biotools:bowtie2
    - doi:10.1038/nmeth.1923
