{% set name = "HISAT2" %}
{% set version = "2.2.0" %}

package:
  name: "{{ name|lower }}"
  version: "{{ version }}"

source:
  url: https://github.com/DaehwanKimLab/hisat2/archive/v{{ version }}.tar.gz
  sha256: 429882d90ad9c600a986279b3ca5d78573caacf3bf0d780c802c006d4fcf0a01

build:
  number: 4

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

test:
  commands:
    - hisat2 --help
    - hisatgenotype_extract_reads.py --help

about:
  home: http://daehwankimlab.github.io/hisat2
  license: GPL-3.0
  license_family: GPL
  license_file: LICENSE
  summary: "Graph-based alignment of next generation sequencing reads to a population of genomes."
  description: "HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome."
  doc_url: https://daehwankimlab.github.io/hisat2/manual/
  dev_url: https://github.com/DaehwanKimLab/hisat2

extra:
  identifiers:
    - biotools:HISAT2
    - doi:10.1038/nmeth.3317
    - doi:10.1038/s41587-019-0201-4
  notes: "Pre-built indices for HISAT2 can be downloaded from https://daehwankimlab.github.io/hisat2/download/."
