# This file created by conda-build 3.21.8
# meta.yaml template originally from:
# /opt/recipe, last modified Thu Sep 15 15:15:59 2022
# ------------------------------------------------

package:
  name: rgi
  version: 6.0.0
source:
  - sha256: f93c87e70715717c71689f2416b1b9886714f10d9ffb9df95f6899c0ea9e8333
    url: https://github.com/arpcard/rgi/archive/6.0.0.tar.gz
  - folder: card-data
    sha256: dd02b8c6d86fc1c3c83402a8985b765eeacd80c9f10d200138e775adc793fb08
    url: https://card.mcmaster.ca/download/0/broadstreet-v3.2.5.tar.bz2
build:
  noarch: python
  number: '0'
  string: pyha8f3691_0
requirements:
  host:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 2_gnu
    - bamtools 2.5.1 hd03093a_10
    - beautifulsoup4 4.9.3 pyhb0f4dca_0
    - bedtools 2.30.0 h468198e_3
    - biopython 1.78 py38h497a2fe_2
    - blast 2.9.0 pl526he19e7b1_7
    - bokeh 2.4.3 pyhd8ed1ab_3
    - bowtie2 2.4.5 py38h77f66f0_4
    - brotli 1.0.9 h166bdaf_7
    - brotli-bin 1.0.9 h166bdaf_7
    - brotlipy 0.7.0 py38h0a891b7_1004
    - bwa 0.7.17 h7132678_9
    - bzip2 1.0.8 h7f98852_4
    - c-ares 1.18.1 h7f98852_0
    - ca-certificates 2022.9.14 ha878542_0
    - certifi 2022.9.14 pyhd8ed1ab_0
    - cffi 1.14.4 py38ha312104_0
    - chardet 3.0.4 py38h924ce5b_1008
    - click 8.1.3 py38h578d9bd_0
    - cloudpickle 2.2.0 pyhd8ed1ab_0
    - cryptography 37.0.4 py38h2b5fc30_0
    - curl 7.83.1 h7bff187_0
    - cycler 0.11.0 pyhd8ed1ab_0
    - cytoolz 0.12.0 py38h0a891b7_0
    - dask 2022.9.0 pyhd8ed1ab_0
    - dask-core 2022.9.0 pyhd8ed1ab_0
    - diamond 0.8.36 h5b5514e_6
    - distributed 2022.9.0 pyhd8ed1ab_0
    - entrez-direct 16.2 he881be0_1
    - filetype 1.1.0 pyhd8ed1ab_0
    - fonttools 4.37.1 py38h0a891b7_0
    - freetype 2.12.1 hca18f0e_0
    - fsspec 2022.8.2 pyhd8ed1ab_0
    - gettext 0.19.8.1 hf34092f_1004
    - giflib 5.2.1 h36c2ea0_2
    - heapdict 1.0.1 py_0
    - htslib 1.9 h4da6232_3
    - icu 70.1 h27087fc_0
    - idna 2.10 pyh9f0ad1d_0
    - jbig 2.1 h7f98852_2003
    - jinja2 3.1.2 pyhd8ed1ab_1
    - jpeg 9e h166bdaf_2
    - keyutils 1.6.1 h166bdaf_0
    - kiwisolver 1.4.4 py38h43d8883_0
    - kma 1.4.3 h7132678_1
    - krb5 1.19.3 h3790be6_0
    - lcms2 2.12 hddcbb42_0
    - ld_impl_linux-64 2.36.1 hea4e1c9_2
    - lerc 2.2.1 h9c3ff4c_0
    - libblas 3.9.0 16_linux64_openblas
    - libbrotlicommon 1.0.9 h166bdaf_7
    - libbrotlidec 1.0.9 h166bdaf_7
    - libbrotlienc 1.0.9 h166bdaf_7
    - libcblas 3.9.0 16_linux64_openblas
    - libcurl 7.83.1 h7bff187_0
    - libdeflate 1.7 h7f98852_5
    - libedit 3.1.20191231 h46ee950_2
    - libev 4.33 h516909a_1
    - libffi 3.2.1 he1b5a44_1007
    - libgcc-ng 12.1.0 h8d9b700_16
    - libgfortran-ng 12.1.0 h69a702a_16
    - libgfortran5 12.1.0 hdcd56e2_16
    - libgomp 12.1.0 h8d9b700_16
    - libiconv 1.16 h516909a_0
    - libidn2 2.3.3 h166bdaf_0
    - liblapack 3.9.0 16_linux64_openblas
    - libnghttp2 1.47.0 hdcd2b5c_1
    - libopenblas 0.3.21 pthreads_h78a6416_3
    - libpng 1.6.37 h753d276_4
    - libssh2 1.10.0 haa6b8db_3
    - libstdcxx-ng 12.1.0 ha89aaad_16
    - libtiff 4.3.0 hf544144_1
    - libunistring 0.9.10 h7f98852_0
    - libwebp 1.2.2 h3452ae3_0
    - libwebp-base 1.2.2 h7f98852_1
    - libxcb 1.13 h7f98852_1004
    - libxml2 2.9.14 h22db469_4
    - libxslt 1.1.35 h8affb1d_0
    - libzlib 1.2.12 h166bdaf_3
    - locket 1.0.0 pyhd8ed1ab_0
    - lxml 4.6.5 py38hf1fe3a4_0
    - lz4 4.0.0 py38h1bf946c_2
    - lz4-c 1.9.3 h9c3ff4c_1
    - markupsafe 2.1.1 py38h0a891b7_1
    - matplotlib-base 3.5.3 py38h38b5ce0_2
    - msgpack-python 1.0.4 py38h43d8883_0
    - munkres 1.1.4 pyh9f0ad1d_0
    - ncurses 6.1 hf484d3e_1002
    - numpy 1.23.3 py38h3a7f9d9_0
    - oligoarrayaux 3.8 hc9558a2_0
    - openjpeg 2.4.0 hb52868f_1
    - openssl 1.1.1q h166bdaf_0
    - packaging 21.3 pyhd8ed1ab_0
    - pandas 1.4.4 py38h47df419_0
    - partd 1.3.0 pyhd8ed1ab_0
    - patsy 0.5.2 pyhd8ed1ab_0
    - pcre 8.45 h9c3ff4c_0
    - perl 5.26.2 h36c2ea0_1008
    - perl-archive-tar 2.32 pl526_0
    - perl-carp 1.38 pl526_3
    - perl-common-sense 3.74 pl526_2
    - perl-compress-raw-bzip2 2.087 pl526he1b5a44_0
    - perl-compress-raw-zlib 2.087 pl526hc9558a2_0
    - perl-exporter 5.72 pl526_1
    - perl-exporter-tiny 1.002001 pl526_0
    - perl-extutils-makemaker 7.36 pl526_1
    - perl-io-compress 2.087 pl526he1b5a44_0
    - perl-io-zlib 1.10 pl526_2
    - perl-json 4.02 pl526_0
    - perl-json-xs 2.34 pl526h6bb024c_3
    - perl-list-moreutils 0.428 pl526_1
    - perl-list-moreutils-xs 0.428 pl526_0
    - perl-pathtools 3.75 pl526h14c3975_1
    - perl-scalar-list-utils 1.52 pl526h516909a_0
    - perl-types-serialiser 1.0 pl526_2
    - perl-xsloader 0.24 pl526_0
    - pillow 9.1.1 py38h0ee0e06_1
    - pip 22.2.2 pyhd8ed1ab_0
    - prodigal 2.6.3 hec16e2b_4
    - psutil 5.9.2 py38h0a891b7_0
    - pthread-stubs 0.4 h36c2ea0_1001
    - pyahocorasick 1.4.4 py38h0a891b7_2
    - pycparser 2.21 pyhd8ed1ab_0
    - pyfaidx 0.7.1 pyh5e36f6f_0
    - pyopenssl 22.0.0 pyhd8ed1ab_0
    - pyparsing 3.0.9 pyhd8ed1ab_0
    - pysam 0.16.0.1 py38hf7546f9_3
    - pysocks 1.7.1 pyha2e5f31_6
    - python 3.8.6 h852b56e_0_cpython
    - python-dateutil 2.8.2 pyhd8ed1ab_0
    - python_abi 3.8 2_cp38
    - pytz 2022.2.1 pyhd8ed1ab_0
    - pyvcf3 1.0.3 pyhdfd78af_0
    - pyyaml 6.0 py38h0a891b7_4
    - readline 8.0 h46ee950_1
    - requests 2.24.0 pyh9f0ad1d_0
    - samtools 1.9 h10a08f8_12
    - scipy 1.9.1 py38hea3f02b_0
    - seaborn 0.12.0 hd8ed1ab_0
    - seaborn-base 0.12.0 pyhd8ed1ab_0
    - setuptools 65.3.0 pyhd8ed1ab_1
    - six 1.16.0 pyh6c4a22f_0
    - sortedcontainers 2.4.0 pyhd8ed1ab_0
    - soupsieve 2.3.2.post1 pyhd8ed1ab_0
    - sqlite 3.39.2 h5082296_0
    - statsmodels 0.13.2 py38h71d37f0_0
    - tbb 2021.5.0 h924138e_2
    - tblib 1.7.0 pyhd8ed1ab_0
    - tk 8.6.12 h27826a3_0
    - toolz 0.12.0 pyhd8ed1ab_0
    - tornado 6.1 py38h0a891b7_3
    - typing_extensions 4.3.0 pyha770c72_0
    - unicodedata2 14.0.0 py38h0a891b7_1
    - urllib3 1.25.11 py_0
    - wget 1.20.3 ha56f1ee_1
    - wheel 0.37.1 pyhd8ed1ab_0
    - xorg-libxau 1.0.9 h7f98852_0
    - xorg-libxdmcp 1.1.3 h7f98852_0
    - xz 5.2.6 h166bdaf_0
    - yaml 0.2.5 h7f98852_2
    - zict 2.2.0 pyhd8ed1ab_0
    - zlib 1.2.12 h166bdaf_3
    - zstd 1.5.2 h6239696_4
  run:
    - bamtools >=2.5.1,<2.5.2.0a0
    - beautifulsoup4==4.9.3
    - bedtools >=2.28.0
    - biopython 1.78.*
    - blast 2.9.0.*
    - bowtie2 >=2.3.4.3
    - bwa >=0.7.17
    - dask
    - diamond 0.8.36.*
    - filetype >=1.0.0
    - kma >=1.2.26
    - lxml==4.6.5
    - matplotlib-base >=2.1.2
    - oligoarrayaux 3.8.*
    - pandas >=0.15.0
    - prodigal 2.6.3.*
    - pyahocorasick >=1.1.7
    - pyfaidx >=0.5.4.1
    - pysam==0.16.0.1
    - python >=3.5
    - requests==2.24.0
    - samtools 1.9.*
    - seaborn >=0.8.1
    - six >=1.7.0
    - wget
    - zlib >=1.2.12,<1.3.0a0
test:
  commands:
    - rgi database -v
    - rgi load -h
    - rgi auto_load -h
    - rgi main -h
    - rgi tab -h
    - rgi parser -h
    - rgi clean -h
    - rgi galaxy -h
    - rgi bwt -h
    - rgi kmer_build -h
    - rgi kmer_query -h
    - wget --quiet --output-document=homolog.fasta https://raw.githubusercontent.com/arpcard/rgi/master/tests/inputs/homolog.fasta
      | rgi main -i homolog.fasta -o output --debug -a diamond --clean
about:
  home: https://card.mcmaster.ca
  license: https://card.mcmaster.ca/about
  license_file: LICENSE
  summary: This tool provides a preliminary annotation of your DNA sequence(s) based
    upon the data available in The Comprehensive Antibiotic Resistance Database (CARD).
    Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted.
    As CARD expands to include more pathogens, genomes, plasmids, and ontology terms
    this tool will grow increasingly powerful in providing first-pass detection of
    antibiotic resistance associated genes. See license at CARD website
extra:
  copy_test_source_files: true
  final: true
  identifiers:
    - doi:10.1093/nar/gkz935
