# This file created by conda-build 3.21.4
# meta.yaml template originally from:
# /opt/recipe, last modified Tue Oct 12 11:25:53 2021
# ------------------------------------------------

package:
  name: hiline
  version: 0.2.4
source:
  sha256: e6e24c09c1b88898a0b91be086d35a5c04f60af27ba845976bd60409fde61f0b
  url: https://github.com/wtsi-hpag/HiLine/archive/0.2.4.tar.gz
build:
  number: '0'
  script: /opt/conda/conda-bld/hiline_1634038392216/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/bin/python
    -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv
  string: py39h8aee962_0
requirements:
  build:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 1_gnu
    - 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
    - clang 12.0.1 ha770c72_4
    - clang-12 12.0.1 default_ha53f305_4
    - cmake 3.21.3 h8897547_0
    - curl 7.79.1 h494985f_1
    - expat 2.4.1 h9c3ff4c_0
    - gcc_impl_linux-64 9.4.0 h03d3576_10
    - gcc_linux-64 9.4.0 h391b98a_1
    - gettext 0.19.8.1 h73d1719_1008
    - git 2.33.0 pl5321hf874766_2
    - gxx_impl_linux-64 9.4.0 h03d3576_10
    - 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
    - libclang-cpp12 12.0.1 default_ha53f305_4
    - libcurl 7.79.1 h494985f_1
    - libedit 3.1.20191231 he28a2e2_2
    - libev 4.33 h516909a_1
    - libffi 3.4.2 h9c3ff4c_4
    - libgcc-devel_linux-64 9.4.0 hd854feb_10
    - libgcc-ng 11.2.0 h1d223b6_10
    - libgomp 11.2.0 h1d223b6_10
    - libiconv 1.16 h516909a_0
    - libllvm12 12.0.1 hf817b99_2
    - libnghttp2 1.43.0 ha19adfc_1
    - libsanitizer 9.4.0 h79bfe98_10
    - libssh2 1.10.0 ha35d2d1_2
    - libstdcxx-devel_linux-64 9.4.0 hd854feb_10
    - libstdcxx-ng 11.2.0 he4da1e4_10
    - libuv 1.42.0 h7f98852_0
    - libzlib 1.2.11 h36c2ea0_1013
    - lz4-c 1.9.3 h9c3ff4c_1
    - ncurses 6.2 h58526e2_4
    - openssl 3.0.0 h7f98852_1
    - pcre2 10.37 h032f7d1_0
    - perl 5.32.1 1_h7f98852_perl5
    - pip 21.3 pyhd8ed1ab_0
    - pkg-config 0.29.2 h36c2ea0_1008
    - pkgconfig 1.5.5 py39hf3d152e_0
    - python 3.9.7 hf930737_3_cpython
    - python_abi 3.9 2_cp39
    - readline 8.1 h46c0cb4_0
    - rhash 1.4.1 h7f98852_0
    - setuptools 58.2.0 py39hf3d152e_0
    - sqlite 3.36.0 h9cd32fc_2
    - sysroot_linux-64 2.12 he073ed8_14
    - tk 8.6.11 h27826a3_1
    - tzdata 2021c he74cb21_0
    - wheel 0.37.0 pyhd8ed1ab_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
    - boost-cpp 1.74.0 h312852a_4
    - bzip2 1.0.8 h7f98852_4
    - ca-certificates 2021.10.8 ha878542_0
    - icu 68.1 h58526e2_0
    - ld_impl_linux-64 2.36.1 hea4e1c9_2
    - libblas 3.9.0 11_linux64_openblas
    - libcblas 3.9.0 11_linux64_openblas
    - libffi 3.4.2 h9c3ff4c_4
    - libgcc-ng 11.2.0 h1d223b6_10
    - libgfortran-ng 11.2.0 h69a702a_10
    - libgfortran5 11.2.0 h5c6108e_10
    - libgomp 11.2.0 h1d223b6_10
    - liblapack 3.9.0 11_linux64_openblas
    - libopenblas 0.3.17 pthreads_h8fe5266_1
    - libstdcxx-ng 11.2.0 he4da1e4_10
    - libzlib 1.2.11 h36c2ea0_1013
    - lz4-c 1.9.3 h9c3ff4c_1
    - ncurses 6.2 h58526e2_4
    - ninja 1.10.2 h4bd325d_1
    - numpy 1.21.2 py39hdbf815f_0
    - openssl 3.0.0 h7f98852_1
    - pcre 8.45 h9c3ff4c_0
    - pip 21.3 pyhd8ed1ab_0
    - python 3.9.7 hf930737_3_cpython
    - python_abi 3.9 2_cp39
    - ragel 6.10 hf484d3e_1002
    - readline 8.1 h46c0cb4_0
    - setuptools 58.2.0 py39hf3d152e_0
    - sqlite 3.36.0 h9cd32fc_2
    - tk 8.6.11 h27826a3_1
    - tzdata 2021c he74cb21_0
    - wheel 0.37.0 pyhd8ed1ab_1
    - xz 5.2.5 h516909a_1
    - zlib 1.2.11 h36c2ea0_1013
    - zstd 1.5.0 ha95c52a_0
  run:
    - biopython >=1.76
    - bwa >=0.7.17
    - bwa-mem2 >=2.0
    - click >=7.0
    - gawk >=5.1.0
    - libgcc-ng >=9.4.0
    - libstdcxx-ng >=9.4.0
    - matplotlib-base >=3.2.0
    - minimap2 >=2.17
    - numpy >=1.21.2,<2.0a0
    - pandas >=1.0.1
    - pcre >=8.45,<9.0a0
    - perl >=5.30.3
    - python >=3.9,<3.10.0a0
    - python_abi 3.9.* *_cp39
    - samtools >=1.10
    - seaborn >=0.10.0
test:
  commands:
    - HiLine --help
  imports:
    - HiLine
about:
  description: 'This is a HiC short-read alignment pipeline. It will perform an alignment,
    or read in an external alignment, perform optional duplicate-read marking, perform
    HiC read classification based on an in-slico restriction digest of reference sequences
    and finally split the output alignments based on HiC read-type. It can also optionally
    process and output HiC alignment statistics. Under the hood, it uses bwa mem and
    samtools to perform and process alignments. It also uses a custom C++ Python extension
    to perform the in-silico digest (using the Hyperscan (https://github.com/intel/hyperscan)
    regex library) and subsequent HiC classification.

    '
  home: https://github.com/wtsi-hpag/HiLine
  license: MIT
  license_family: MIT
  license_file: LICENSE
  summary: HiC alignment and classification pipeline.
extra:
  copy_test_source_files: true
  final: true
