{% set name = "trinity" %}
{% set version = "2.8.5" %}

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

source:
  url: https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v{{ version }}.tar.gz
  sha256: eef3691aee5dbc73d8ce609f82912d3d0ae81eabced5fa61d1e53dbfe37cf3dc
  patches:
    - patch

build:
  number: 4
  skip: True  # [osx]

requirements:
  build:
    - {{ compiler('cxx') }}
    - {{ compiler('c') }}
    - cmake
    - autoconf
  host:
    - zlib
  run:
    - trimmomatic >=0.36
    - bowtie
    - bowtie2 >=2.3.0
    - kmer-jellyfish >=2.2
    - openjdk >=8
    - perl
    - python
    - samtools >=1.3
    - zlib
    - salmon >=0.9.1,<1.0
    - numpy

test:
  commands:
    - "Trinity --cite"
    - "align_and_estimate_abundance.pl --help || [[ \"$?\" == 255 ]]"
    - "abundance_estimates_to_matrix.pl --help || [[ \"$?\" == 255 ]]"
    - "run_DE_analysis.pl -h || [[ \"$?\" == 255 ]]"
    - "analyze_diff_expr.pl -h || [[ \"$?\" == 255 ]]"
    - "PtR --help || [[ \"$?\" == 255 ]]"
    - "TrinityStats.pl 2>&1 | grep \"usage:\""
    - "define_clusters_by_cutting_tree.pl 2>&1 | grep \"define K clusters via k-means algorithm\""
    - "Trinity_gene_splice_modeler.py --help"

about:
  home: https://github.com/trinityrnaseq/trinityrnaseq/
  license: 'BSD-3-Clause'
  summary: 'Trinity RNA-Seq de novo transcriptome assembly'

extra:
  identifiers:
    - biotools:trinity
