build:
  number: 3
# OSX build skipped because of this error: https://gist.github.com/pvanheus/2fbce93b326a3edb1a57aaebc8ca749e
  skip: True # [osx]

package:
  name: trinity
  version: '2.6.6'

requirements:
  build:
    - {{ compiler('cxx') }}
  host:
    - collectl
    - fastool
    - jellyfish >=2.2.6
    - openjdk
    - parafly
    - perl-app-cpanminus
    - perl-module-build
    - samtools >=1.3
    - slclust
    - trimmomatic >=0.36
    - zlib

  run:
    - bowtie
    - bowtie2 >=2.3.0
    - collectl
    - fastool
    - jellyfish >=2.2.6
    - openjdk
    - parafly
    - perl-app-cpanminus
    - perl-module-build
    - samtools >=1.3
    - slclust
    - trimmomatic >=0.36
    - zlib
    - salmon >=0.9.1

source:
  url: https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.6.6.tar.gz
  sha256: 868dfadeefaf2d3c6150a88d5e86fbc09466d69bbf4a65f70b4f5a7485668984
  patches:
    - chrysalis.bioconda.patch

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

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

extra:
  identifiers:
    - biotools:trinity
