# This file created by conda-build 3.21.4
# meta.yaml template originally from:
# /opt/recipe, last modified Mon Oct 25 20:47:36 2021
# ------------------------------------------------

package:
  name: trinity
  version: 2.12.0
source:
  patches:
    - makefile.patch
  sha256: 0d47dc433cc3003e1c732b97da605e29c6ccafa38cd52cdb8ecc42399a9195d0
  url: https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v2.12.0/trinityrnaseq-v2.12.0.FULL.tar.gz
build:
  number: '3'
  string: ha140323_3
requirements:
  build:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 1_gnu
    - autoconf 2.69 pl5321hd708f79_11
    - binutils_impl_linux-64 2.36.1 h193b22a_2
    - binutils_linux-64 2.36 hf3e587d_1
    - bzip2 1.0.8 h7f98852_4
    - c-ares 1.17.2 h7f98852_0
    - ca-certificates 2021.10.8 ha878542_0
    - cmake 3.21.3 h8897547_0
    - expat 2.4.1 h9c3ff4c_0
    - gcc_impl_linux-64 9.4.0 h03d3576_11
    - gcc_linux-64 9.4.0 h391b98a_1
    - gxx_impl_linux-64 9.4.0 h03d3576_11
    - gxx_linux-64 9.4.0 h0316aca_1
    - kernel-headers_linux-64 2.6.32 he073ed8_14
    - krb5 1.19.2 h48eae69_2
    - ld_impl_linux-64 2.36.1 hea4e1c9_2
    - libcurl 7.79.1 h494985f_1
    - libedit 3.1.20191231 he28a2e2_2
    - libev 4.33 h516909a_1
    - libgcc-devel_linux-64 9.4.0 hd854feb_11
    - libgcc-ng 11.2.0 h1d223b6_11
    - libgomp 11.2.0 h1d223b6_11
    - libnghttp2 1.43.0 ha19adfc_1
    - libsanitizer 9.4.0 h79bfe98_11
    - libssh2 1.10.0 ha35d2d1_2
    - libstdcxx-devel_linux-64 9.4.0 hd854feb_11
    - libstdcxx-ng 11.2.0 he4da1e4_11
    - libuv 1.42.0 h7f98852_0
    - libzlib 1.2.11 h36c2ea0_1013
    - lz4-c 1.9.3 h9c3ff4c_1
    - m4 1.4.18 h516909a_1001
    - make 4.3 hd18ef5c_1
    - ncurses 6.2 h58526e2_4
    - openssl 3.0.0 h7f98852_1
    - perl 5.32.1 1_h7f98852_perl5
    - rhash 1.4.1 h7f98852_0
    - sysroot_linux-64 2.12 he073ed8_14
    - tk 8.6.11 h27826a3_1
    - xz 5.2.5 h516909a_1
    - zlib 1.2.11 h36c2ea0_1013
    - zstd 1.5.0 ha95c52a_0
  host:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 1_gnu
    - bzip2 1.0.8 h7f98852_4
    - c-ares 1.17.2 h7f98852_0
    - ca-certificates 2021.10.8 ha878542_0
    - htslib 1.12 h9093b5e_1
    - krb5 1.19.2 hcc1bbae_2
    - libcurl 7.79.1 h2574ce0_1
    - libdeflate 1.7 h7f98852_5
    - libedit 3.1.20191231 he28a2e2_2
    - libev 4.33 h516909a_1
    - libgcc-ng 11.2.0 h1d223b6_11
    - libgomp 11.2.0 h1d223b6_11
    - libnghttp2 1.43.0 h812cca2_1
    - libssh2 1.10.0 ha56f1ee_2
    - libstdcxx-ng 11.2.0 he4da1e4_11
    - libzlib 1.2.11 h36c2ea0_1013
    - ncurses 6.2 h58526e2_4
    - openssl 1.1.1l h7f98852_0
    - tk 8.6.11 h27826a3_1
    - xz 5.2.5 h516909a_1
    - zlib 1.2.11 h36c2ea0_1013
  run:
    - _openmp_mutex >=4.5
    - bioconductor-ctc
    - bioconductor-dexseq
    - bioconductor-edger
    - bioconductor-go.db
    - bioconductor-goseq
    - bioconductor-qvalue
    - bowtie
    - bowtie2 >=2.3.0
    - coreutils
    - htslib >=1.12,<1.13.0a0
    - htslib >=1.12,<1.13.0a0
    - kallisto
    - kmer-jellyfish >=2.2
    - libgcc-ng >=9.4.0
    - libstdcxx-ng >=9.4.0
    - libzlib >=1.2.11,<1.3.0a0
    - numpy
    - openjdk >=8
    - perl
    - python >=3.6
    - r-ape
    - r-argparse
    - r-base >=4
    - r-cluster
    - r-fastcluster
    - r-gplots
    - r-phangorn
    - r-sm
    - r-tidyverse
    - r-vioplot
    - salmon >=1.0
    - samtools >=1.9
    - trimmomatic >=0.36
    - zlib >=1.2.11,<1.3.0a0
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
    - LICENSE.txt
  summary: Trinity assembles transcript sequences from Illumina RNA-Seq data.
extra:
  copy_test_source_files: true
  final: true
  identifiers:
    - biotools:trinity
    - doi:10.1038/nbt.1883
    - usegalaxy-eu:trinity
