# This file created by conda-build 24.7.1
# meta.yaml template originally from:
# /opt/recipe, last modified Thu May 29 07:39:00 2025
# ------------------------------------------------

package:
  name: trinity
  version: 2.15.2
source:
  patches:
    - 0003-installer.patch
    - cflags-remove-m64.patch
    - makefile.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 >=2.15.2,<3.0a0
  string: pl5321h1e84f2d_4
requirements:
  build:
    - _openmp_mutex 4.5 2_gnu
    - binutils_impl_linux-aarch64 2.43 h4c662bb_4
    - binutils_linux-aarch64 2.43 hf1166c9_4
    - bzip2 1.0.8 h68df207_7
    - c-ares 1.34.5 h86ecc28_0
    - ca-certificates 2025.4.26 hbd8a1cb_0
    - cmake 4.0.2 h0efca9c_0
    - gcc_impl_linux-aarch64 13.3.0 h80a1502_2
    - gcc_linux-aarch64 13.3.0 h1cd514b_10
    - gxx_impl_linux-aarch64 13.3.0 h7eae8fb_2
    - gxx_linux-aarch64 13.3.0 h2864abd_10
    - kernel-headers_linux-aarch64 4.18.0 h05a177a_18
    - keyutils 1.6.1 h4e544f5_0
    - krb5 1.21.3 h50a48e9_0
    - ld_impl_linux-aarch64 2.43 h80caac9_4
    - libcurl 8.14.0 h6702fde_0
    - libedit 3.1.20250104 pl5321h976ea20_0
    - libev 4.33 h31becfc_2
    - libexpat 2.7.0 h5ad3122_0
    - libgcc 15.1.0 he277a41_2
    - libgcc-devel_linux-aarch64 13.3.0 h0c07274_102
    - libgcc-ng 15.1.0 he9431aa_2
    - libgomp 15.1.0 he277a41_2
    - liblzma 5.8.1 h86ecc28_1
    - libnghttp2 1.64.0 hc8609a4_0
    - libsanitizer 13.3.0 ha58e236_2
    - libssh2 1.11.1 h18c354c_0
    - libstdcxx 15.1.0 h3f4de04_2
    - libstdcxx-devel_linux-aarch64 13.3.0 h0c07274_102
    - libstdcxx-ng 15.1.0 hf1166c9_2
    - libuv 1.51.0 h86ecc28_0
    - libzlib 1.3.1 h86ecc28_2
    - make 4.4.1 h2a6d0cb_2
    - ncurses 6.5 ha32ae93_3
    - openssl 3.5.0 hd08dc88_1
    - rhash 1.4.6 h86ecc28_0
    - sysroot_linux-aarch64 2.17 h68829e0_18
    - tzdata 2025b h78e105d_0
    - zstd 1.5.7 hbcf94c1_2
  host:
    - _openmp_mutex 4.5 2_gnu
    - bzip2 1.0.8 h68df207_7
    - c-ares 1.34.5 h86ecc28_0
    - ca-certificates 2025.4.26 hbd8a1cb_0
    - htslib 1.21 h7068f72_1
    - keyutils 1.6.1 h4e544f5_0
    - krb5 1.21.3 h50a48e9_0
    - libcurl 8.14.0 h6702fde_0
    - libdeflate 1.22 h86ecc28_0
    - libedit 3.1.20250104 pl5321h976ea20_0
    - libev 4.33 h31becfc_2
    - libgcc 15.1.0 he277a41_2
    - libgcc-ng 15.1.0 he9431aa_2
    - libgomp 15.1.0 he277a41_2
    - libiconv 1.18 hc99b53d_1
    - liblzma 5.8.1 h86ecc28_1
    - libnghttp2 1.64.0 hc8609a4_0
    - libssh2 1.11.1 h18c354c_0
    - libstdcxx 15.1.0 h3f4de04_2
    - libstdcxx-ng 15.1.0 hf1166c9_2
    - libxcrypt 4.4.36 h31becfc_1
    - libzlib 1.3.1 h86ecc28_2
    - lz4-c 1.10.0 h5ad3122_1
    - ncurses 6.5 ha32ae93_3
    - openssl 3.5.0 hd08dc88_1
    - perl 5.32.1 7_h31becfc_perl5
    - popt 1.16 h57fc80e_2002
    - rsync 3.4.1 hdfa5021_2
    - xxhash 0.8.3 hd794028_0
    - zlib 1.3.1 h86ecc28_2
    - zstd 1.5.7 hbcf94c1_2
  run:
    - _openmp_mutex >=4.5
    - bioconductor-ctc
    - bioconductor-dexseq
    - bioconductor-edger
    - bioconductor-go.db
    - bioconductor-goseq
    - bioconductor-qvalue
    - bowtie2 >=2.3.0
    - coreutils
    - htslib >=1.21,<1.22.0a0
    - kallisto
    - kmer-jellyfish >=2.3
    - libgcc >=13
    - libgomp
    - libstdcxx >=13
    - libzlib >=1.3.1,<2.0a0
    - numpy
    - openjdk >=17
    - perl >=5.32.1,<5.33.0a0 *_perl5
    - perl-db_file
    - python >=3.7
    - r-ape
    - r-argparse
    - r-base
    - r-cluster
    - r-fastcluster
    - r-gplots
    - r-phangorn
    - r-sm
    - r-tidyverse
    - r-vioplot
    - salmon
    - samtools >=1.14
    - trimmomatic >=0.39
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
  copy_test_source_files: true
  final: true
  identifiers:
    - biotools:trinity
    - doi:10.1038/nbt.1883
    - doi:10.1038/nprot.2013.084
    - usegalaxy-eu:trinity
