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

build:
  number: 8
  skip: True # [osx]


package:
  name: trinity
  version: '2.2.0'

requirements:
  build:
    - {{ compiler('cxx') }}
  host:
    - perl-app-cpanminus
    - perl-module-build
    - perl-file-find-rule
    - java-jdk
    - zlib
    - jellyfish 2.2.3
    - samtools 0.1.19
    - trimmomatic
    - collectl
    - fastool
    - parafly
    - slclust
  run:
    - perl-app-cpanminus
    - perl-module-build
    - perl-file-find-rule
    - java-jdk
    - zlib
    - jellyfish 2.2.3
    - samtools 0.1.19
    - trimmomatic
    - bowtie
    - collectl
    - fastool
    - parafly
    - slclust

source:
  url: https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.2.0.tar.gz
  patches:
    - makefile.clean.patch
    - trinity-plugins.makefile.clean.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"
    - "contig_ExN50_statistic.pl 2>&1 | grep \"usage:\" &> /dev/null"


extra:
  identifiers:
    - biotools:trinity

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