# This file created by conda-build 3.24.0
# meta.yaml template originally from:
# /opt/recipe, last modified Mon May 15 05:57:49 2023
# ------------------------------------------------

package:
  name: quast
  version: 5.2.0
source:
  patches:
    - genemark-issue_disable-and-exclude-from-package.patch
    - remove-explicit-dependencies-from-setup-py.patch
    - skip-glimmer-in-test.patch
  sha256: ccd911087cfa254ad4b8eadac4f95d4685e44c3996f5516b8e0ce6f7cfa7e0db
  url:
    - http://downloads.sourceforge.net/project/quast/quast-5.2.0.tar.gz
    - https://github.com/ablab/quast/releases/download/quast_5.2.0/quast-5.2.0.tar.gz
build:
  number: '3'
  string: py38pl5321h5cf8b27_3
requirements:
  build:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 2_gnu
    - binutils_impl_linux-64 2.39 he00db2b_1
    - binutils_linux-64 2.39 h5fc0e48_13
    - gcc_impl_linux-64 12.2.0 hcc96c02_19
    - gcc_linux-64 12.2.0 h4798a0e_13
    - gxx_impl_linux-64 12.2.0 hcc96c02_19
    - gxx_linux-64 12.2.0 hb41e900_13
    - kernel-headers_linux-64 2.6.32 he073ed8_15
    - ld_impl_linux-64 2.39 hcc3a1bd_1
    - libgcc-devel_linux-64 12.2.0 h3b97bd3_19
    - libgcc-ng 12.2.0 h65d4601_19
    - libgomp 12.2.0 h65d4601_19
    - libsanitizer 12.2.0 h46fd767_19
    - libstdcxx-devel_linux-64 12.2.0 h3b97bd3_19
    - libstdcxx-ng 12.2.0 h46fd767_19
    - make 4.3 hd18ef5c_1
    - sysroot_linux-64 2.12 he073ed8_15
  host:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 2_gnu
    - blast 2.14.0 hf3cf87c_0
    - brotli 1.0.9 h166bdaf_8
    - brotli-bin 1.0.9 h166bdaf_8
    - bzip2 1.0.8 h7f98852_4
    - c-ares 1.18.1 h7f98852_0
    - ca-certificates 2023.5.7 hbcca054_0
    - certifi 2023.5.7 pyhd8ed1ab_0
    - circos 0.69.9 hdfd78af_0
    - contourpy 1.0.7 py38hfbd4bf9_0
    - curl 7.88.1 hdc1c0ab_1
    - cycler 0.11.0 pyhd8ed1ab_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
    - fonttools 4.39.4 py38h01eb140_0
    - freetype 2.12.1 hca18f0e_1
    - gettext 0.21.1 h27087fc_0
    - giflib 5.2.1 h0b41bf4_3
    - glimmerhmm 3.0.4 pl5321h87f3376_5
    - icu 72.1 hcb278e6_0
    - importlib-resources 5.12.0 pyhd8ed1ab_0
    - importlib_resources 5.12.0 pyhd8ed1ab_0
    - joblib 1.2.0 pyhd8ed1ab_0
    - k8 0.2.5 hdcf5f25_3
    - keyutils 1.6.1 h166bdaf_0
    - kiwisolver 1.4.4 py38h43d8883_1
    - krb5 1.20.1 h81ceb04_0
    - lcms2 2.15 haa2dc70_1
    - ld_impl_linux-64 2.40 h41732ed_0
    - lerc 4.0.0 h27087fc_0
    - libblas 3.9.0 16_linux64_openblas
    - libbrotlicommon 1.0.9 h166bdaf_8
    - libbrotlidec 1.0.9 h166bdaf_8
    - libbrotlienc 1.0.9 h166bdaf_8
    - libcblas 3.9.0 16_linux64_openblas
    - libcurl 7.88.1 hdc1c0ab_1
    - 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 12.2.0 h65d4601_19
    - libgd 2.3.3 hfa28ad5_6
    - libgfortran-ng 12.2.0 h69a702a_19
    - libgfortran5 12.2.0 h337968e_19
    - libgomp 12.2.0 h65d4601_19
    - libidn2 2.3.4 h166bdaf_0
    - libjpeg-turbo 2.1.5.1 h0b41bf4_0
    - liblapack 3.9.0 16_linux64_openblas
    - libnghttp2 1.52.0 h61bc06f_0
    - libnsl 2.0.0 h7f98852_0
    - libopenblas 0.3.21 pthreads_h78a6416_3
    - libpng 1.6.39 h753d276_0
    - libsqlite 3.41.2 h2797004_1
    - libssh2 1.10.0 hf14f497_3
    - libstdcxx-ng 12.2.0 h46fd767_19
    - libtiff 4.5.0 ha587672_6
    - libunistring 0.9.10 h7f98852_0
    - libuuid 2.38.1 h0b41bf4_0
    - libwebp 1.3.0 hb47c5f0_0
    - libwebp-base 1.3.0 h0b41bf4_0
    - libxcb 1.13 h7f98852_1004
    - libzlib 1.2.13 h166bdaf_4
    - matplotlib-base 3.7.1 py38hd6c3c57_0
    - minimap2 2.26 h7132678_0
    - munkres 1.1.4 pyh9f0ad1d_0
    - ncurses 6.3 h27087fc_1
    - numpy 1.24.3 py38h59b608b_0
    - openjpeg 2.5.0 hfec8fc6_2
    - openssl 3.1.0 hd590300_3
    - packaging 23.1 pyhd8ed1ab_0
    - pcre 8.45 h9c3ff4c_0
    - perl 5.32.1 2_h7f98852_perl5
    - perl-archive-tar 2.40 pl5321hdfd78af_0
    - perl-b-cow 0.007 pl5321h166bdaf_0
    - perl-carp 1.50 pl5321hd8ed1ab_0
    - perl-clone 0.46 pl5321h166bdaf_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-config-general 2.65 pl5321hdfd78af_0
    - perl-digest-perl-md5 1.9 pl5321hdfd78af_2
    - perl-encode 3.19 pl5321h166bdaf_0
    - perl-exporter 5.74 pl5321hd8ed1ab_0
    - perl-exporter-tiny 1.002002 pl5321hd8ed1ab_0
    - perl-extutils-config 0.008 pl5321ha770c72_0
    - perl-extutils-helpers 0.026 pl5321ha770c72_0
    - perl-extutils-installpaths 0.012 pl5321ha770c72_0
    - perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0
    - perl-extutils-pl2bat 0.005 pl5321ha770c72_0
    - perl-font-ttf 1.06 pl5321hdfd78af_1
    - perl-gd 2.76 pl5321h5b5514e_1
    - perl-inc-latest 0.500 pl5321ha770c72_0
    - perl-io-compress 2.201 pl5321hdbdd923_1
    - perl-io-string 1.08 pl5321hdfd78af_4
    - perl-io-zlib 1.14 pl5321hdfd78af_0
    - perl-json 4.10 pl5321hdfd78af_0
    - perl-json-xs 2.34 pl5321h9f5acd7_5
    - perl-list-moreutils 0.430 pl5321hdfd78af_0
    - perl-list-moreutils-xs 0.430 pl5321h031d066_2
    - perl-math-bezier 0.01 pl5321hdfd78af_2
    - perl-math-round 0.07 pl5321ha770c72_0
    - perl-math-vecstat 0.08 pl5321hdfd78af_2
    - perl-module-build 0.4234 pl5321ha770c72_0
    - perl-module-build-tiny 0.039 pl5321h166bdaf_0
    - perl-module-implementation 0.09 pl5321ha770c72_0
    - perl-module-runtime 0.016 pl5321hdfd78af_2
    - perl-number-format 1.75 pl5321hdfd78af_4
    - perl-params-validate 1.31 pl5321h031d066_1
    - perl-parent 0.241 pl5321hd8ed1ab_0
    - perl-pathtools 3.75 pl5321h166bdaf_0
    - perl-readonly 2.05 pl5321ha770c72_0
    - perl-regexp-common 2017060201 pl5321hd8ed1ab_0
    - perl-scalar-list-utils 1.63 pl5321h166bdaf_0
    - perl-set-intspan 1.19 pl5321hdfd78af_2
    - perl-statistics-basic 1.6611 pl5321hdfd78af_3
    - perl-storable 3.15 pl5321h166bdaf_0
    - perl-svg 2.87 pl5321hd8ed1ab_0
    - perl-test-fatal 0.016 pl5321ha770c72_0
    - perl-text-format 0.62 pl5321hdfd78af_0
    - perl-time-hires 1.9764 pl5321h031d066_3
    - perl-try-tiny 0.31 pl5321ha770c72_0
    - perl-types-serialiser 1.01 pl5321hdfd78af_0
    - perl-xml-parser 2.44_01 pl5321hc3e0081_1003
    - pillow 9.5.0 py38h961100d_0
    - pip 23.1.2 pyhd8ed1ab_0
    - pthread-stubs 0.4 h36c2ea0_1001
    - pyparsing 3.0.9 pyhd8ed1ab_0
    - python 3.8.16 he550d4f_1_cpython
    - python-dateutil 2.8.2 pyhd8ed1ab_0
    - python_abi 3.8 3_cp38
    - readline 8.2 h8228510_1
    - setuptools 67.7.2 pyhd8ed1ab_0
    - simplejson 3.19.1 py38h1de0b5d_0
    - six 1.16.0 pyh6c4a22f_0
    - tk 8.6.12 h27826a3_0
    - unicodedata2 15.0.0 py38h0a891b7_0
    - wget 1.20.3 ha35d2d1_1
    - wheel 0.40.0 pyhd8ed1ab_0
    - xorg-libxau 1.0.9 h7f98852_0
    - xorg-libxdmcp 1.1.3 h7f98852_0
    - xz 5.2.6 h166bdaf_0
    - zipp 3.15.0 pyhd8ed1ab_0
    - zlib 1.2.13 h166bdaf_4
    - zstd 1.5.2 h3eb15da_6
  run:
    - bedtools
    - blast
    - bwa
    - circos
    - glimmerHMM
    - joblib
    - libgcc-ng >=12
    - libstdcxx-ng >=12
    - libzlib >=1.2.13,<1.3.0a0
    - matplotlib-base
    - minimap2 >=2.10
    - openjdk >=8
    - perl >=5.32.1,<5.33.0a0 *_perl5
    - python >=3.8,<3.9.0a0
    - python_abi 3.8.* *_cp38
    - simplejson
test:
  commands:
    - quast --version
    - metaquast --version
  source_files:
    - test_data
about:
  home: http://quast.sourceforge.net/
  license: Custom
  license_file: LICENSE.txt
  summary: Quality Assessment Tool for Genome Assemblies
extra:
  container:
    extended-base: true
  copy_test_source_files: true
  final: true
  identifiers:
    - biotools:quast
    - doi:10.1093/bioinformatics/btt086
  notes: '- GeneMark gene prediction software is disabled due to licensing issues

    '
