# This file created by conda-build 3.24.0
# meta.yaml template originally from:
# /opt/recipe, last modified Thu Aug 10 15:00:11 2023
# ------------------------------------------------

package:
  name: busco
  version: 5.5.0
source:
  patches:
    - 0001-Add-default-config-path-within-prefix-updated.patch
  sha256: 07ca32892ddd6016e5610c34f830cc8445dbcade3f7b460c3d898e27c9650cc7
  url: https://gitlab.com/ezlab/busco/-/archive/5.5.0/busco-5.5.0.tar.gz
build:
  noarch: python
  number: '0'
  string: pyhdfd78af_0
requirements:
  host:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 2_gnu
    - alsa-lib 1.2.9 hd590300_0
    - augustus 3.5.0 pl5321h700735d_3
    - bamtools 2.5.1 hd03093a_10
    - bbmap 39.01 h92535d8_1
    - biopython 1.81 py39h72bdee0_0
    - blast 2.14.0 pl5321h6f7f691_2
    - boost-cpp 1.78.0 h6582d0a_3
    - bzip2 1.0.8 h7f98852_4
    - c-ares 1.19.1 hd590300_0
    - ca-certificates 2023.7.22 hbcca054_0
    - cairo 1.16.0 hbbf8b49_1016
    - cdbtools 0.99 hdcf5f25_9
    - curl 7.87.0 h6312ad2_0
    - dendropy 4.5.2 pyh3252c3a_0
    - diamond 2.1.8 h43eeafb_0
    - entrez-direct 16.2 he881be0_1
    - expat 2.5.0 hcb278e6_1
    - font-ttf-dejavu-sans-mono 2.37 hab24e00_0
    - font-ttf-inconsolata 3.000 h77eed37_0
    - font-ttf-source-code-pro 2.038 h77eed37_0
    - font-ttf-ubuntu 0.83 hab24e00_0
    - fontconfig 2.14.2 h14ed4e7_0
    - fonts-conda-ecosystem 1 0
    - fonts-conda-forge 1 0
    - freetype 2.12.1 hca18f0e_1
    - gawk 5.1.0 h7f98852_0
    - gettext 0.21.1 h27087fc_0
    - giflib 5.2.1 h0b41bf4_3
    - gmp 6.2.1 h58526e2_0
    - graphite2 1.3.13 h58526e2_1001
    - gsl 2.7 he838d99_0
    - harfbuzz 7.3.0 hdb3a94d_0
    - hmmer 3.1b2 3
    - htslib 1.17 h6bc39ce_1
    - icu 72.1 hcb278e6_0
    - keyutils 1.6.1 h166bdaf_0
    - krb5 1.20.1 hf9c8cef_0
    - lcms2 2.15 haa2dc70_1
    - ld_impl_linux-64 2.40 h41732ed_0
    - lerc 4.0.0 h27087fc_0
    - libblas 3.9.0 17_linux64_openblas
    - libcblas 3.9.0 17_linux64_openblas
    - libcups 2.3.3 h36d4200_3
    - libcurl 7.87.0 h6312ad2_0
    - libdeflate 1.18 h0b41bf4_0
    - libedit 3.1.20191231 he28a2e2_2
    - libev 4.33 h516909a_1
    - libexpat 2.5.0 hcb278e6_1
    - libffi 3.4.2 h7f98852_5
    - libgcc-ng 13.1.0 he5830b7_0
    - libgfortran-ng 13.1.0 h69a702a_0
    - libgfortran5 13.1.0 h15d22d2_0
    - libglib 2.76.4 hebfc3b9_0
    - libgomp 13.1.0 he5830b7_0
    - libhwloc 2.9.2 nocuda_h7313eea_1008
    - libiconv 1.17 h166bdaf_0
    - libidn2 2.3.4 h166bdaf_0
    - libjpeg-turbo 2.1.5.1 h0b41bf4_0
    - liblapack 3.9.0 17_linux64_openblas
    - libnghttp2 1.51.0 hdcd2b5c_0
    - libnsl 2.0.0 h7f98852_0
    - libopenblas 0.3.23 pthreads_h80387f5_0
    - libpng 1.6.39 h753d276_0
    - libsqlite 3.42.0 h2797004_0
    - libssh2 1.10.0 haa6b8db_3
    - libstdcxx-ng 13.1.0 hfd8a6a1_0
    - libtiff 4.5.1 h8b53f26_0
    - libunistring 0.9.10 h7f98852_0
    - libuuid 2.38.1 h0b41bf4_0
    - libwebp-base 1.3.1 hd590300_0
    - libxcb 1.15 h0b41bf4_0
    - libxml2 2.11.5 h0d562d8_0
    - libzlib 1.2.13 hd590300_5
    - lp_solve 5.5.2.5 h14c3975_1001
    - metaeuk 6.a5d39d9 pl5321h6a68c12_3
    - metis 5.1.1 h59595ed_0
    - miniprot 0.12 he4a0461_0
    - mpfr 4.2.0 hb012696_0
    - mysql-connector-c 6.1.11 h6eb9d5d_1007
    - ncbi-vdb 3.0.0 pl5321h87f3376_0
    - ncurses 6.4 hcb278e6_0
    - numpy 1.25.2 py39h6183b62_0
    - openjdk 20.0.0 h8e330f5_0
    - openssl 1.1.1v hd590300_0
    - pandas 2.0.3 py39h40cae4c_1
    - pbzip2 1.1.13 0
    - pcre 8.45 h9c3ff4c_0
    - pcre2 10.40 hc3806b6_0
    - perl 5.32.1 4_hd590300_perl5
    - perl-app-cpanminus 1.7047 pl5321hd8ed1ab_0
    - perl-archive-tar 2.40 pl5321hdfd78af_0
    - perl-carp 1.50 pl5321hd8ed1ab_0
    - perl-class-method-modifiers 2.13 pl5321ha770c72_0
    - perl-common-sense 3.75 pl5321hd8ed1ab_0
    - perl-compress-raw-bzip2 2.201 pl5321h166bdaf_0
    - perl-compress-raw-zlib 2.202 pl5321h166bdaf_0
    - perl-constant 1.33 pl5321hd8ed1ab_0
    - perl-dbi 1.643 pl5321h166bdaf_0
    - perl-encode 3.19 pl5321h166bdaf_0
    - perl-exporter 5.74 pl5321hd8ed1ab_0
    - perl-exporter-tiny 1.002002 pl5321hd8ed1ab_0
    - perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0
    - perl-file-path 2.18 pl5321hd8ed1ab_0
    - perl-file-temp 0.2304 pl5321hd8ed1ab_0
    - perl-file-which 1.24 pl5321hd8ed1ab_0
    - perl-inc-latest 0.500 pl5321ha770c72_0
    - perl-io-compress 2.201 pl5321hdbdd923_2
    - perl-io-zlib 1.14 pl5321hdfd78af_0
    - perl-json 4.10 pl5321hdfd78af_0
    - perl-json-xs 2.34 pl5321h4ac6f70_6
    - perl-list-moreutils 0.430 pl5321hdfd78af_0
    - perl-list-moreutils-xs 0.430 pl5321h031d066_2
    - perl-module-build 0.4234 pl5321ha770c72_0
    - perl-moo 2.005004 pl5321ha770c72_0
    - perl-parallel-forkmanager 2.02 pl5321hdfd78af_1
    - perl-parent 0.241 pl5321hd8ed1ab_0
    - perl-pathtools 3.75 pl5321h166bdaf_0
    - perl-role-tiny 2.002004 pl5321ha770c72_0
    - perl-scalar-list-utils 1.63 pl5321h166bdaf_0
    - perl-storable 3.15 pl5321h166bdaf_0
    - perl-sub-quote 2.006006 pl5321ha770c72_0
    - perl-test-fatal 0.016 pl5321ha770c72_0
    - perl-try-tiny 0.31 pl5321ha770c72_0
    - perl-types-serialiser 1.01 pl5321hdfd78af_0
    - perl-yaml 1.30 pl5321hdfd78af_0
    - pip 23.2.1 pyhd8ed1ab_0
    - pixman 0.40.0 h36c2ea0_0
    - prodigal 2.6.3 h031d066_6
    - pthread-stubs 0.4 h36c2ea0_1001
    - python 3.9.15 h47a2c10_0_cpython
    - python-dateutil 2.8.2 pyhd8ed1ab_0
    - python-tzdata 2023.3 pyhd8ed1ab_0
    - python_abi 3.9 3_cp39
    - pytz 2023.3 pyhd8ed1ab_0
    - readline 8.2 h8228510_1
    - rocm-smi 5.6.0 h59595ed_1
    - samtools 1.17 hd87286a_1
    - sepp 4.4.0 py39_0
    - setuptools 68.0.0 pyhd8ed1ab_0
    - six 1.16.0 pyh6c4a22f_0
    - sqlite 3.42.0 h2c6b66d_0
    - suitesparse 5.10.1 h9e50725_1
    - tar 1.34 hb2e2bae_1
    - tbb 2021.10.0 h00ab1b0_0
    - tk 8.6.12 h27826a3_0
    - tzdata 2023c h71feb2d_0
    - ucsc-fatotwobit 447 h954228d_0
    - ucsc-twobitinfo 447 h954228d_0
    - wget 1.20.3 ha56f1ee_1
    - wheel 0.41.1 pyhd8ed1ab_0
    - xorg-fixesproto 5.0 h7f98852_1002
    - xorg-inputproto 2.3.2 h7f98852_1002
    - xorg-kbproto 1.0.7 h7f98852_1002
    - xorg-libice 1.1.1 hd590300_0
    - xorg-libsm 1.2.4 h7391055_0
    - xorg-libx11 1.8.6 h8ee46fc_0
    - xorg-libxau 1.0.11 hd590300_0
    - xorg-libxdmcp 1.1.3 h7f98852_0
    - xorg-libxext 1.3.4 h0b41bf4_2
    - xorg-libxfixes 5.0.3 h7f98852_1004
    - xorg-libxi 1.7.10 h7f98852_0
    - xorg-libxrender 0.9.11 hd590300_0
    - xorg-libxt 1.3.0 hd590300_1
    - xorg-libxtst 1.2.3 h7f98852_1002
    - xorg-recordproto 1.14.2 h7f98852_1002
    - xorg-renderproto 0.11.1 h7f98852_1002
    - xorg-xextproto 7.3.0 h0b41bf4_1003
    - xorg-xproto 7.0.31 h7f98852_1007
    - xz 5.2.6 h166bdaf_0
    - zlib 1.2.13 hd590300_5
    - zstd 1.5.2 hfc55251_7
  run:
    - augustus >=3.3
    - bbmap
    - biopython
    - blast >=2.10.1
    - dendropy <4.6.0
    - fonts-conda-ecosystem
    - hmmer >=3.1b2
    - metaeuk >=6.a5d39d9
    - miniprot
    - pandas
    - prodigal
    - python >=3.3
    - r-base
    - r-ggplot2 >=2.2.1
    - sepp >=4.3.10
    - wget
test:
  commands:
    - busco -h
    - generate_plot.py -h
  source_files:
    - test_data
about:
  description: BUSCO provides measures for quantitative assessment of genome assembly,
    gene set, and transcriptome completeness based on evolutionarily informed expectations
    of gene content from near-universal single-copy orthologs selected from OrthoDB.
  home: http://busco.ezlab.org/
  license: MIT
  license_file: LICENSE
  summary: Assessment of assembly completeness using Universal Single Copy Orthologs
extra:
  container:
    extended-base: true
  copy_test_source_files: true
  final: true
  identifiers:
    - biotools:busco
    - doi:10.1093/bioinformatics/btv351
    - usegalaxy-eu:busco
  recipe-maintainers:
    - berkelem
    - matsepp
    - silask
