<commit_before>{% set name = "Trinity" %}
{% set version = "2.9.1" %}
{% set sha256 = "98d98bc21cd5dd32b408ed52586d01a15873b49b96de3264d42616bdcfc9d455" %}

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

source:
  url: https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v2.9.1/trinityrnaseq-v{{ version }}.FULL.tar.gz
  sha256: {{ sha256 }}
  patches:
    - makefile.patch

build:
  number: 0
  skip: True  # [osx]

requirements:
  build:
    - {{ compiler('cxx') }}
    - {{ compiler('c') }}
    - cmake
    - autoconf
  host:
    - zlib
  run:
    - zlib
    - trimmomatic >=0.36
    - bowtie
    - bowtie2 >=2.3.0
    - kmer-jellyfish >=2.2
    - openjdk >=8
    - perl
    - python >=3.6
    - samtools >=1.9
    - salmon >=0.11.2
    - 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"
<commit_msg>[ci skip] Merge PR 20234<commit_after>{% set name = "Trinity" %}
{% set version = "2.9.1" %}
{% set sha256 = "98d98bc21cd5dd32b408ed52586d01a15873b49b96de3264d42616bdcfc9d455" %}

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

source:
  url: https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v2.9.1/trinityrnaseq-v{{ version }}.FULL.tar.gz
  sha256: {{ sha256 }}
  patches:
    - makefile.patch

build:
  number: 1
  skip: True  # [osx]

requirements:
  build:
    - {{ compiler('cxx') }}
    - {{ compiler('c') }}
    - cmake
    - autoconf
  host:
    - zlib
  run:
    - zlib
    - trimmomatic >=0.36
    - bowtie
    - bowtie2 >=2.3.0
    - kmer-jellyfish >=2.2
    - openjdk >=8
    - perl
    - python >=3.6
    - samtools >=1.9
    - salmon >=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"

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