# This file created by conda-build 24.7.1
# meta.yaml template originally from:
# /opt/recipe, last modified Mon Dec 30 23:05:22 2024
# ------------------------------------------------

package:
  name: bioconductor-cogito
  version: 1.12.0
source:
  md5: 8854881ef6815a33908f11ebd03c81ab
  url:
    - https://bioarchive.galaxyproject.org/Cogito_1.12.0.tar.gz
    - https://bioconductor.org/packages/3.20/bioc/src/contrib/Archive/Cogito/Cogito_1.12.0.tar.gz
    - https://bioconductor.org/packages/3.20/bioc/src/contrib/Cogito_1.12.0.tar.gz
    - https://depot.galaxyproject.org/software/bioconductor-cogito/bioconductor-cogito_1.12.0_src_all.tar.gz
build:
  noarch: generic
  number: '0'
  rpaths:
    - lib/
    - lib/R/lib/
  run_exports: bioconductor-cogito >=1.12.0,<1.13.0a0
  string: r44hdfd78af_0
requirements:
  host:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 2_gnu
    - _r-mutex 1.0.1 anacondar_1
    - argcomplete 3.5.2 pyhd8ed1ab_0
    - binutils_impl_linux-64 2.43 h4bf12b8_2
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    - bioconductor-biobase 2.66.0 r44h3df3fcb_0
    - bioconductor-biocgenerics 0.52.0 r44hdfd78af_0
    - bioconductor-biocio 1.16.0 r44hdfd78af_0
    - bioconductor-biocparallel 1.40.0 r44he5774e6_0
    - bioconductor-biostrings 2.74.0 r44h3df3fcb_0
    - bioconductor-data-packages 20241220 hdfd78af_0
    - bioconductor-delayedarray 0.32.0 r44h3df3fcb_0
    - bioconductor-genomeinfodb 1.42.0 r44hdfd78af_0
    - bioconductor-genomeinfodbdata 1.2.13 r44hdfd78af_0
    - bioconductor-genomicalignments 1.42.0 r44h3df3fcb_0
    - bioconductor-genomicfeatures 1.58.0 r44hdfd78af_0
    - bioconductor-genomicranges 1.58.0 r44h3df3fcb_0
    - bioconductor-iranges 2.40.0 r44h3df3fcb_0
    - bioconductor-keggrest 1.46.0 r44hdfd78af_0
    - bioconductor-matrixgenerics 1.18.0 r44hdfd78af_0
    - bioconductor-rhtslib 3.2.0 r44h15a9599_1
    - bioconductor-rsamtools 2.22.0 r44h77050f0_0
    - bioconductor-rtracklayer 1.66.0 r44h15a9599_0
    - bioconductor-s4arrays 1.6.0 r44h3df3fcb_0
    - bioconductor-s4vectors 0.44.0 r44h3df3fcb_0
    - bioconductor-sparsearray 1.6.0 r44h3df3fcb_0
    - bioconductor-summarizedexperiment 1.36.0 r44hdfd78af_0
    - bioconductor-txdb.mmusculus.ucsc.mm9.knowngene 3.2.2 r44hdfd78af_17
    - bioconductor-ucsc.utils 1.2.0 r44hdfd78af_0
    - bioconductor-xvector 0.46.0 r44h15a9599_0
    - bioconductor-zlibbioc 1.52.0 r44h3df3fcb_0
    - bwidget 1.10.1 ha770c72_0
    - bzip2 1.0.8 h4bc722e_7
    - c-ares 1.34.4 hb9d3cd8_0
    - ca-certificates 2024.12.14 hbcca054_0
    - cairo 1.18.2 h3394656_1
    - curl 8.11.1 h332b0f4_0
    - font-ttf-dejavu-sans-mono 2.37 hab24e00_0
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    - font-ttf-source-code-pro 2.038 h77eed37_0
    - font-ttf-ubuntu 0.83 h77eed37_3
    - fontconfig 2.15.0 h7e30c49_1
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    - fonts-conda-forge 1 0
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    - fribidi 1.0.10 h36c2ea0_0
    - gcc_impl_linux-64 14.2.0 h6b349bd_1
    - gfortran_impl_linux-64 14.2.0 hc73f493_1
    - graphite2 1.3.13 h59595ed_1003
    - gsl 2.7 he838d99_0
    - gxx_impl_linux-64 14.2.0 h2c03514_1
    - harfbuzz 10.1.0 h0b3b770_0
    - icu 75.1 he02047a_0
    - jq 1.7.1 hd590300_0
    - kernel-headers_linux-64 3.10.0 he073ed8_18
    - keyutils 1.6.1 h166bdaf_0
    - krb5 1.21.3 h659f571_0
    - ld_impl_linux-64 2.43 h712a8e2_2
    - lerc 4.0.0 h27087fc_0
    - libblas 3.9.0 26_linux64_openblas
    - libcblas 3.9.0 26_linux64_openblas
    - libcurl 8.11.1 h332b0f4_0
    - libdeflate 1.23 h4ddbbb0_0
    - libedit 3.1.20191231 he28a2e2_2
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    - libexpat 2.6.4 h5888daf_0
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    - libgcc 14.2.0 h77fa898_1
    - libgcc-devel_linux-64 14.2.0 h41c2201_101
    - libgcc-ng 14.2.0 h69a702a_1
    - libgfortran 14.2.0 h69a702a_1
    - libgfortran-ng 14.2.0 h69a702a_1
    - libgfortran5 14.2.0 hd5240d6_1
    - libglib 2.82.2 h2ff4ddf_0
    - libgomp 14.2.0 h77fa898_1
    - libiconv 1.17 hd590300_2
    - libjpeg-turbo 3.0.0 hd590300_1
    - liblapack 3.9.0 26_linux64_openblas
    - liblzma 5.6.3 hb9d3cd8_1
    - libmpdec 4.0.0 h4bc722e_0
    - libnghttp2 1.64.0 h161d5f1_0
    - libopenblas 0.3.28 pthreads_h94d23a6_1
    - libpng 1.6.44 hadc24fc_0
    - libsanitizer 14.2.0 h2a3dede_1
    - libsqlite 3.47.2 hee588c1_0
    - libssh2 1.11.1 hf672d98_0
    - libstdcxx 14.2.0 hc0a3c3a_1
    - libstdcxx-devel_linux-64 14.2.0 h41c2201_101
    - libstdcxx-ng 14.2.0 h4852527_1
    - libtiff 4.7.0 hd9ff511_3
    - libuuid 2.38.1 h0b41bf4_0
    - libwebp-base 1.5.0 h851e524_0
    - libxcb 1.17.0 h8a09558_0
    - libxml2 2.13.5 h8d12d68_1
    - libzlib 1.3.1 hb9d3cd8_2
    - make 4.4.1 hb9d3cd8_2
    - ncurses 6.5 he02047a_1
    - oniguruma 6.9.9 hd590300_0
    - openssl 3.4.0 hb9d3cd8_0
    - pandoc 3.6.1 ha770c72_0
    - pango 1.54.0 h861ebed_4
    - pcre2 10.44 hba22ea6_2
    - pip 24.3.1 pyh145f28c_2
    - pixman 0.44.2 h29eaf8c_0
    - pthread-stubs 0.4 hb9d3cd8_1002
    - python 3.13.1 ha99a958_102_cp313
    - python_abi 3.13 5_cp313
    - pyyaml 6.0.2 py313h536fd9c_1
    - r-abind 1.4_5 r44hc72bb7e_1006
    - r-askpass 1.2.1 r44h2b5f3a1_0
    - r-base 4.4.2 hc737e89_2
    - r-base64enc 0.1_3 r44hb1dbf0f_1007
    - r-bh 1.87.0_1 r44hc72bb7e_0
    - r-biocmanager 1.30.25 r44hc72bb7e_0
    - r-bit 4.5.0.1 r44h2b5f3a1_0
    - r-bit64 4.5.2 r44h2b5f3a1_0
    - r-bitops 1.0_9 r44h2b5f3a1_0
    - r-blob 1.2.4 r44hc72bb7e_2
    - r-bslib 0.8.0 r44hc72bb7e_0
    - r-cachem 1.1.0 r44hb1dbf0f_1
    - r-cli 3.6.3 r44h0d4f4ea_1
    - r-codetools 0.2_20 r44hc72bb7e_1
    - r-colorspace 2.1_1 r44hdb488b9_0
    - r-cpp11 0.5.1 r44hc72bb7e_0
    - r-crayon 1.5.3 r44hc72bb7e_1
    - r-curl 6.0.1 r44h2700575_0
    - r-dbi 1.2.3 r44hc72bb7e_1
    - r-digest 0.6.37 r44h0d4f4ea_0
    - r-ellipsis 0.3.2 r44hb1dbf0f_3
    - r-entropy 1.3.1 r44hc72bb7e_3
    - r-evaluate 1.0.1 r44hc72bb7e_0
    - r-fansi 1.0.6 r44hb1dbf0f_1
    - r-farver 2.1.2 r44ha18555a_1
    - r-fastmap 1.2.0 r44ha18555a_1
    - r-fontawesome 0.5.3 r44hc72bb7e_0
    - r-formatr 1.14 r44hc72bb7e_2
    - r-fs 1.6.5 r44h93ab643_0
    - r-futile.logger 1.4.3 r44hc72bb7e_1006
    - r-futile.options 1.0.1 r44hc72bb7e_1005
    - r-ggplot2 3.5.1 r44hc72bb7e_1
    - r-glue 1.8.0 r44h2b5f3a1_0
    - r-gtable 0.3.6 r44hc72bb7e_0
    - r-highr 0.11 r44hc72bb7e_1
    - r-htmltools 0.5.8.1 r44ha18555a_1
    - r-httr 1.4.7 r44hc72bb7e_1
    - r-isoband 0.2.7 r44ha18555a_3
    - r-jquerylib 0.1.4 r44hc72bb7e_3
    - r-jsonlite 1.8.9 r44h2b5f3a1_0
    - r-knitr 1.49 r44hc72bb7e_0
    - r-labeling 0.4.3 r44hc72bb7e_1
    - r-lambda.r 1.2.4 r44hc72bb7e_4
    - r-lattice 0.22_6 r44hb1dbf0f_1
    - r-lifecycle 1.0.4 r44hc72bb7e_1
    - r-magrittr 2.0.3 r44hb1dbf0f_3
    - r-mass 7.3_60.0.1 r44hb1dbf0f_1
    - r-matrix 1.6_5 r44he966344_1
    - r-matrixstats 1.4.1 r44h2b5f3a1_0
    - r-memoise 2.0.1 r44hc72bb7e_3
    - r-mgcv 1.9_1 r44h0d28552_1
    - r-mime 0.12 r44hb1dbf0f_3
    - r-munsell 0.5.1 r44hc72bb7e_1
    - r-nlme 3.1_165 r44hbcb9c34_1
    - r-openssl 2.2.2 r44he8289e2_0
    - r-pillar 1.10.0 r44hc72bb7e_0
    - r-pkgconfig 2.0.3 r44hc72bb7e_4
    - r-plogr 0.2.0 r44hc72bb7e_1006
    - r-png 0.1_8 r44h21f035c_2
    - r-r6 2.5.1 r44hc72bb7e_3
    - r-rappdirs 0.3.3 r44hb1dbf0f_3
    - r-rcolorbrewer 1.1_3 r44h785f33e_3
    - r-rcurl 1.98_1.16 r44he8228da_1
    - r-restfulr 0.0.15 r44h5ef9028_5
    - r-rjson 0.2.23 r44h93ab643_0
    - r-rlang 1.1.4 r44ha18555a_1
    - r-rmarkdown 2.29 r44hc72bb7e_0
    - r-rsqlite 2.3.9 r44h93ab643_0
    - r-sass 0.4.9 r44ha18555a_1
    - r-scales 1.3.0 r44hc72bb7e_1
    - r-snow 0.4_4 r44hc72bb7e_3
    - r-sys 3.4.3 r44h2b5f3a1_0
    - r-tibble 3.2.1 r44hdb488b9_3
    - r-tinytex 0.54 r44hc72bb7e_0
    - r-utf8 1.2.4 r44hb1dbf0f_1
    - r-vctrs 0.6.5 r44h0d4f4ea_1
    - r-viridislite 0.4.2 r44hc72bb7e_2
    - r-withr 3.0.2 r44hc72bb7e_0
    - r-xfun 0.49 r44h93ab643_0
    - r-xml 3.99_0.17 r44h5bae778_2
    - r-yaml 2.3.10 r44hdb488b9_0
    - readline 8.2 h8228510_1
    - sed 4.8 he412f7d_0
    - setuptools 75.6.0 pyhff2d567_1
    - sysroot_linux-64 2.17 h0157908_18
    - tk 8.6.13 noxft_h4845f30_101
    - tktable 2.10 h8bc8fbc_6
    - toml 0.10.2 pyhd8ed1ab_1
    - tomlkit 0.13.2 pyha770c72_1
    - tzdata 2024b hc8b5060_0
    - xmltodict 0.14.2 pyhd8ed1ab_1
    - xorg-libice 1.1.2 hb9d3cd8_0
    - xorg-libsm 1.2.5 he73a12e_0
    - xorg-libx11 1.8.10 h4f16b4b_1
    - xorg-libxau 1.0.12 hb9d3cd8_0
    - xorg-libxdmcp 1.1.5 hb9d3cd8_0
    - xorg-libxext 1.3.6 hb9d3cd8_0
    - xorg-libxrender 0.9.12 hb9d3cd8_0
    - xorg-libxt 1.3.1 hb9d3cd8_0
    - yaml 0.2.5 h7f98852_2
    - yq 3.4.3 pyhd8ed1ab_1
    - zstd 1.5.6 ha6fb4c9_0
  run:
    - bioconductor-annotationdbi >=1.68.0,<1.69.0
    - bioconductor-genomeinfodb >=1.42.0,<1.43.0
    - bioconductor-genomicfeatures >=1.58.0,<1.59.0
    - bioconductor-genomicranges >=1.58.0,<1.59.0
    - bioconductor-s4vectors >=0.44.0,<0.45.0
    - bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0
    - r-base >=4.4,<4.5.0a0
    - r-base >=4.4,<4.5.0a0
    - r-biocmanager
    - r-entropy
    - r-ggplot2
    - r-jsonlite
    - r-magrittr
    - r-rmarkdown
test:
  commands:
    - $R -e "library('Cogito')"
about:
  description: Biological studies often consist of multiple conditions which are examined
    with different laboratory set ups like RNA-sequencing or ChIP-sequencing. To get
    an overview about the whole resulting data set, Cogito provides an automated,
    complete, reproducible and clear report about all samples and basic comparisons
    between all different samples. This report can be used as documentation about
    the data set or as starting point for further custom analysis.
  home: https://bioconductor.org/packages/3.20/bioc/html/Cogito.html
  license: LGPL-3
  license_file: /opt/conda/conda-bld/bioconductor-cogito_1735605020300/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/share/licenses/LGPL-3
  summary: Compare genomic intervals tool - Automated, complete, reproducible and
    clear report about genomic and epigenomic data sets
extra:
  copy_test_source_files: true
  final: true
