# This file created by conda-build 24.7.1
# meta.yaml template originally from:
# /opt/recipe, last modified Wed Mar 19 13:17:29 2025
# ------------------------------------------------

package:
  name: bioconductor-deepsnv
  version: 1.52.0
source:
  md5: 23f4830f8b5ad3b1c38ef91ad6427a9a
  url:
    - https://bioarchive.galaxyproject.org/deepSNV_1.52.0.tar.gz
    - https://bioconductor.org/packages/3.20/bioc/src/contrib/Archive/deepSNV/deepSNV_1.52.0.tar.gz
    - https://bioconductor.org/packages/3.20/bioc/src/contrib/deepSNV_1.52.0.tar.gz
    - https://depot.galaxyproject.org/software/bioconductor-deepsnv/bioconductor-deepsnv_1.52.0_src_all.tar.gz
build:
  number: '1'
  rpaths:
    - lib/
    - lib/R/lib/
  run_exports: bioconductor-deepsnv >=1.52.0,<1.53.0a0
  string: r44h6e81ef9_1
requirements:
  build:
    - _openmp_mutex 4.5 2_gnu
    - binutils_impl_linux-aarch64 2.43 h4c662bb_4
    - binutils_linux-aarch64 2.43 hf1166c9_4
    - gcc_impl_linux-aarch64 13.3.0 h80a1502_2
    - gcc_linux-aarch64 13.3.0 h1cd514b_8
    - gxx_impl_linux-aarch64 13.3.0 h7eae8fb_2
    - gxx_linux-aarch64 13.3.0 h2864abd_8
    - kernel-headers_linux-aarch64 4.18.0 h05a177a_18
    - ld_impl_linux-aarch64 2.43 h80caac9_4
    - libgcc 14.2.0 he277a41_2
    - libgcc-devel_linux-aarch64 13.3.0 h0c07274_102
    - libgomp 14.2.0 he277a41_2
    - libsanitizer 13.3.0 ha58e236_2
    - libstdcxx 14.2.0 h3f4de04_2
    - libstdcxx-devel_linux-aarch64 13.3.0 h0c07274_102
    - make 4.4.1 h2a6d0cb_2
    - sysroot_linux-aarch64 2.17 h68829e0_18
    - tzdata 2025a h78e105d_0
  host:
    - _openmp_mutex 4.5 2_gnu
    - _r-mutex 1.0.1 anacondar_1
    - argcomplete 3.6.0 pyhd8ed1ab_0
    - binutils_impl_linux-aarch64 2.43 h4c662bb_4
    - bioconductor-annotationdbi 1.68.0 r44hdfd78af_0
    - bioconductor-biobase 2.66.0 r44h59b44dc_0
    - bioconductor-biocgenerics 0.52.0 r44hdfd78af_3
    - bioconductor-biocio 1.16.0 r44hdfd78af_0
    - bioconductor-biocparallel 1.40.0 r44h12ab77f_1
    - bioconductor-biostrings 2.74.0 r44h59b44dc_1
    - bioconductor-bsgenome 1.74.0 r44hdfd78af_0
    - bioconductor-data-packages 20250105.1 hdfd78af_0
    - bioconductor-delayedarray 0.32.0 r44h59b44dc_1
    - bioconductor-genomeinfodb 1.42.0 r44hdfd78af_2
    - bioconductor-genomeinfodbdata 1.2.13 r44hdfd78af_0
    - bioconductor-genomicalignments 1.42.0 r44h59b44dc_0
    - bioconductor-genomicfeatures 1.58.0 r44hdfd78af_0
    - bioconductor-genomicranges 1.58.0 r44h59b44dc_2
    - bioconductor-iranges 2.40.0 r44h59b44dc_2
    - bioconductor-keggrest 1.46.0 r44hdfd78af_0
    - bioconductor-matrixgenerics 1.18.0 r44hdfd78af_0
    - bioconductor-rhtslib 3.2.0 r44h8793571_1
    - bioconductor-rsamtools 2.22.0 r44h6e81ef9_0
    - bioconductor-rtracklayer 1.66.0 r44h8793571_0
    - bioconductor-s4arrays 1.6.0 r44h59b44dc_0
    - bioconductor-s4vectors 0.44.0 r44h59b44dc_2
    - bioconductor-sparsearray 1.6.0 r44h59b44dc_0
    - bioconductor-summarizedexperiment 1.36.0 r44hdfd78af_0
    - bioconductor-ucsc.utils 1.2.0 r44hdfd78af_0
    - bioconductor-variantannotation 1.52.0 r44h8793571_0
    - bioconductor-xvector 0.46.0 r44h8793571_2
    - bioconductor-zlibbioc 1.52.0 r44h59b44dc_2
    - bwidget 1.10.1 h8af1aa0_0
    - bzip2 1.0.8 h68df207_7
    - c-ares 1.34.4 h86ecc28_0
    - ca-certificates 2025.1.31 hcefe29a_0
    - cairo 1.18.4 h83712da_0
    - curl 8.12.1 h6702fde_0
    - 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 h77eed37_3
    - fontconfig 2.15.0 h8dda3cd_1
    - fonts-conda-ecosystem 1 0
    - fonts-conda-forge 1 0
    - freetype 2.13.3 he93130f_0
    - fribidi 1.0.10 hb9de7d4_0
    - gcc_impl_linux-aarch64 14.2.0 h39ab8d2_2
    - gfortran_impl_linux-aarch64 14.2.0 hf71498c_2
    - graphite2 1.3.13 h2f0025b_1003
    - gsl 2.7 h294027d_0
    - gxx_impl_linux-aarch64 14.2.0 h1262d8f_2
    - harfbuzz 10.4.0 hb5e3f52_0
    - icu 75.1 hf9b3779_0
    - jq 1.7.1 h31becfc_0
    - kernel-headers_linux-aarch64 4.18.0 h05a177a_18
    - keyutils 1.6.1 h4e544f5_0
    - krb5 1.21.3 h50a48e9_0
    - ld_impl_linux-aarch64 2.43 h80caac9_4
    - lerc 4.0.0 h4de3ea5_0
    - libblas 3.9.0 11_hccabdcb_netlib
    - libcblas 3.9.0 11_h8effc92_netlib
    - libcurl 8.12.1 h6702fde_0
    - libdeflate 1.23 h5e3c512_0
    - libedit 3.1.20250104 pl5321h976ea20_0
    - libev 4.33 h31becfc_2
    - libexpat 2.6.4 h5ad3122_0
    - libffi 3.4.6 he21f813_0
    - libgcc 14.2.0 he277a41_2
    - libgcc-devel_linux-aarch64 14.2.0 h46490cb_102
    - libgcc-ng 14.2.0 he9431aa_2
    - libgfortran 14.2.0 he9431aa_2
    - libgfortran-ng 14.2.0 he9431aa_2
    - libgfortran5 14.2.0 hb6113d0_2
    - libglib 2.82.2 hc486b8e_1
    - libgomp 14.2.0 he277a41_2
    - libiconv 1.18 hc99b53d_1
    - libjpeg-turbo 3.0.0 h31becfc_1
    - liblapack 3.9.0 11_ha9b52fb_netlib
    - liblzma 5.6.4 h86ecc28_0
    - liblzma-devel 5.6.4 h86ecc28_0
    - libmpdec 4.0.0 h68df207_0
    - libnghttp2 1.64.0 hc8609a4_0
    - libpng 1.6.47 hec79eb8_0
    - libsanitizer 14.2.0 hff26f3d_2
    - libsqlite 3.49.1 h5eb1b54_2
    - libssh2 1.11.1 ha41c0db_0
    - libstdcxx 14.2.0 h3f4de04_2
    - libstdcxx-devel_linux-aarch64 14.2.0 h46490cb_102
    - libstdcxx-ng 14.2.0 hf1166c9_2
    - libtiff 4.7.0 h88f7998_3
    - libuuid 2.38.1 hb4cce97_0
    - libwebp-base 1.5.0 h0886dbf_0
    - libxcb 1.17.0 h262b8f6_0
    - libxml2 2.13.6 h2e0c361_0
    - libzlib 1.3.1 h86ecc28_2
    - make 4.4.1 h2a6d0cb_2
    - ncurses 6.5 ha32ae93_3
    - oniguruma 6.9.10 h86ecc28_0
    - openssl 3.4.1 hd08dc88_0
    - pango 1.56.3 hd49db62_0
    - pcre2 10.44 h070dd5b_2
    - pip 25.0.1 pyh145f28c_0
    - pixman 0.44.2 h86a87f0_0
    - pthread-stubs 0.4 h86ecc28_1002
    - python 3.13.2 h525b0ce_101_cp313
    - python_abi 3.13 5_cp313
    - pyyaml 6.0.2 py313h857f82b_2
    - r-abind 1.4_5 r44hc72bb7e_1006
    - r-askpass 1.2.1 r44hdd76399_0
    - r-base 4.4.3 h86ec23d_0
    - r-bh 1.87.0_1 r44hc72bb7e_0
    - r-bit 4.6.0 r44hdd76399_0
    - r-bit64 4.6.0_1 r44hdd76399_0
    - r-bitops 1.0_9 r44hdd76399_0
    - r-blob 1.2.4 r44hc72bb7e_2
    - r-cachem 1.1.0 r44hc1cf72c_1
    - r-cli 3.6.4 r44h21d2c02_1
    - r-codetools 0.2_20 r44hc72bb7e_1
    - r-cpp11 0.5.2 r44h785f33e_1
    - r-crayon 1.5.3 r44hc72bb7e_1
    - r-curl 6.2.1 r44h8829f0d_0
    - r-dbi 1.2.3 r44hc72bb7e_1
    - r-fastmap 1.2.0 r44h6170684_1
    - r-formatr 1.14 r44hc72bb7e_2
    - r-futile.logger 1.4.3 r44hc72bb7e_1006
    - r-futile.options 1.0.1 r44hc72bb7e_1005
    - r-glue 1.8.0 r44hdd76399_0
    - r-httr 1.4.7 r44hc72bb7e_1
    - r-jsonlite 1.9.1 r44hdd76399_0
    - r-lambda.r 1.2.4 r44hc72bb7e_4
    - r-lattice 0.22_6 r44hc1cf72c_1
    - r-lifecycle 1.0.4 r44hc72bb7e_1
    - r-matrix 1.7_3 r44h309c413_0
    - r-matrixstats 1.5.0 r44hdd76399_0
    - r-memoise 2.0.1 r44hc72bb7e_3
    - r-mime 0.13 r44hdd76399_0
    - r-openssl 2.3.2 r44hdd99bf7_0
    - r-pkgconfig 2.0.3 r44hc72bb7e_4
    - r-plogr 0.2.0 r44hc72bb7e_1006
    - r-png 0.1_8 r44hb81c312_2
    - r-r6 2.6.1 r44hc72bb7e_0
    - r-rcurl 1.98_1.16 r44ha5cee84_1
    - r-restfulr 0.0.15 r44h475cc98_5
    - r-rjson 0.2.23 r44h9d76b47_0
    - r-rlang 1.1.5 r44h21d2c02_0
    - r-rsqlite 2.3.9 r44h21d2c02_0
    - r-snow 0.4_4 r44hc72bb7e_3
    - r-sys 3.4.3 r44hdd76399_0
    - r-vctrs 0.6.5 r44h6170684_1
    - r-vgam 1.1_13 r44ha805bf2_0
    - r-xml 3.99_0.17 r44hed34aec_2
    - r-yaml 2.3.10 r44hc1cf72c_0
    - readline 8.2 h8382b9d_2
    - sed 4.8 ha0d5d3d_0
    - setuptools 75.8.2 pyhff2d567_0
    - sysroot_linux-aarch64 2.17 h68829e0_18
    - tk 8.6.13 h194ca79_0
    - tktable 2.10 h52f7bd3_6
    - toml 0.10.2 pyhd8ed1ab_1
    - tomlkit 0.13.2 pyha770c72_1
    - tzdata 2025a h78e105d_0
    - xmltodict 0.14.2 pyhd8ed1ab_1
    - xorg-libice 1.1.2 h86ecc28_0
    - xorg-libsm 1.2.6 h0808dbd_0
    - xorg-libx11 1.8.12 hca56bd8_0
    - xorg-libxau 1.0.12 h86ecc28_0
    - xorg-libxdmcp 1.1.5 h57736b2_0
    - xorg-libxext 1.3.6 h57736b2_0
    - xorg-libxrender 0.9.12 h86ecc28_0
    - xorg-libxt 1.3.1 h57736b2_0
    - yaml 0.2.5 hf897c2e_2
    - yq 3.4.3 pyhd8ed1ab_1
    - zlib 1.3.1 h86ecc28_2
    - zstd 1.5.7 hbcf94c1_1
  run:
    - bioconductor-biostrings >=2.74.0,<2.75.0
    - bioconductor-biostrings >=2.74.0,<2.75.0a0
    - bioconductor-genomicranges >=1.58.0,<1.59.0
    - bioconductor-genomicranges >=1.58.0,<1.59.0a0
    - bioconductor-iranges >=2.40.0,<2.41.0
    - bioconductor-iranges >=2.40.0,<2.41.0a0
    - bioconductor-rhtslib >=3.2.0,<3.3.0
    - bioconductor-rhtslib >=3.2.0,<3.3.0a0
    - bioconductor-summarizedexperiment >=1.36.0,<1.37.0
    - bioconductor-summarizedexperiment >=1.36.0,<1.37.0a0
    - bioconductor-variantannotation >=1.52.0,<1.53.0
    - bioconductor-variantannotation >=1.52.0,<1.53.0a0
    - libblas >=3.9.0,<4.0a0
    - libgcc >=13
    - liblapack >=3.9.0,<4.0a0
    - liblzma >=5.6.4,<6.0a0
    - libstdcxx >=13
    - libzlib >=1.3.1,<2.0a0
    - r-base >=4.4,<4.5.0a0
    - r-base >=4.4,<4.5.0a0
    - r-vgam
test:
  commands:
    - $R -e "library('deepSNV')"
about:
  description: This package provides provides quantitative variant callers for detecting
    subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The
    deepSNV algorithm is used for a comparative setup with a control experiment of
    the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate
    sequencing errors and subclonal SNVs. The shearwater algorithm computes a Bayes
    classifier based on a beta-binomial model for variant calling with multiple samples
    for precisely estimating model parameters - such as local error rates and dispersion
    - and prior knowledge, e.g. from variation data bases such as COSMIC.
  home: https://bioconductor.org/packages/3.20/bioc/html/deepSNV.html
  license: GPL-3
  license_file: /opt/conda/conda-bld/bioconductor-deepsnv_1742390473311/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/share/licenses/GPL-3
  summary: Detection of subclonal SNVs in deep sequencing data.
extra:
  additional-platforms:
    - linux-aarch64
  copy_test_source_files: true
  final: true
  identifiers:
    - biotools:deepsnv
