{% set version = "2.9.2" %}
{% set sha256 = "4cb2c0b30292a0a7e6b12f3f5fd865c5962273cb2bc4b4de9f439dfd1c29b385" %}

package:
  name: gridss
  version: '{{ version }}'

source:
  url: https://github.com/PapenfussLab/gridss/releases/download/v{{ version }}/gridss-{{ version }}.tar.gz
  sha256: '{{ sha256 }}'

build:
  number: 0
  noarch: generic

requirements:
  run:
    - openjdk >=8
    - bwa >=0.7
    - samtools >=1.10
    - r-base >=3.6
    - r-argparser
    - r-tidyverse
    - r-testthat
    - r-stringdist
    - bioconductor-structuralvariantannotation

test:
  commands:
    - "gridss 2>&1 | grep 'Usage:'"
    - "gridss_somatic_filter --help 2>&1 | grep 'usage:'"
    - "CallVariants --help 2>&1 | grep 'USAGE:'"
    - "CollectGridssMetrics --help 2>&1 | grep 'USAGE:'"

about:
  home: https://github.com/PapenfussLab/gridss
  license: GPL-3.0
  license_family: GPL
  summary: 'GRIDSS: the Genomic Rearrangement IDentification Software Suite'

extra:
  identifiers:
    - biotools:gridss
    - doi:10.1101/110387
