package:
  name: trinity
  version: 2.15.2
source:
  patches:
    - makefile.patch
    - cflags-remove-m64.patch
    - 0003-installer.patch
  sha256: baab87e4878ad097e265c46de121414629bf88fa9342022baae5cac12432a15c
  url: https://github.com/trinityrnaseq/trinityrnaseq/releases/download/Trinity-v2.15.2/trinityrnaseq-v2.15.2.FULL.tar.gz
build:
  number: '4'
  run_exports:
    - trinity
requirements:
  build:
    - gxx_linux-aarch64 13.*
    - make
    - cmake
  host:
    - libgomp
    - zlib
    - htslib
    - perl
    - rsync
  run:
    - libgomp
    - openjdk >=17
    - perl
    - perl-db_file
    - python >=3.7
    - numpy
    - trimmomatic >=0.39
    - bowtie2 >=2.3.0
    - kmer-jellyfish >=2.3
    - samtools >=1.14
    - salmon
    - kallisto
    - coreutils
    - r-base
    - r-cluster
    - r-gplots
    - r-fastcluster
    - r-argparse
    - r-ape
    - r-phangorn
    - r-gplots
    - r-tidyverse
    - r-sm
    - r-vioplot
    - bioconductor-qvalue
    - bioconductor-ctc
    - bioconductor-edger
    - bioconductor-goseq
    - bioconductor-go.db
    - bioconductor-dexseq
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:
  dev_url: https://github.com/trinityrnaseq/trinityrnaseq
  doc_url: https://github.com/trinityrnaseq/trinityrnaseq/wiki
  home: https://github.com/trinityrnaseq/trinityrnaseq
  license: BSD-3-Clause
  license_family: BSD
  license_file: LICENSE
  summary: Trinity assembles transcript sequences from Illumina RNA-Seq data.
extra:
  additional-platforms:
    - linux-aarch64
  final: false
  identifiers:
    - biotools:trinity
    - usegalaxy-eu:trinity
    - doi:10.1038/nbt.1883
    - doi:10.1038/nprot.2013.084
