# This file created by conda-build 3.15.1
# meta.yaml template originally from:
# /opt/recipe, last modified Tue Oct 23 08:09:37 2018
# ------------------------------------------------

package:
    name: bioconductor-deepsnv
    version: 1.26.1
source:
    sha256: 55036b553920826aeead816e48a8760b756bca513de09a247521b36788aaa01d
    url:
        - http://bioconductor.org/packages/3.7/bioc/src/contrib/deepSNV_1.26.1.tar.gz
        - https://bioarchive.galaxyproject.org/deepSNV_1.26.1.tar.gz
        - https://depot.galaxyproject.org/software/bioconductor-deepsnv/bioconductor-deepsnv_1.26.1_src_all.tar.gz
build:
    number: '0'
    rpaths:
        - lib/
        - lib/R/lib/
    string: r341hfc679d8_0
requirements:
    build:
        - autoconf 2.69 pl526_7
        - automake 1.15.1 pl526_1001
        - libgcc-ng 7.2.0 hdf63c60_3
        - m4 1.4.18 h470a237_1
        - make 4.2.1 h470a237_1002
        - perl 5.26.2 h470a237_0
        - toolchain 2.2.2 0
        - toolchain_c_linux-64 2.2.2 0
        - toolchain_cxx_linux-64 2.2.2 0
    host:
        - bioconductor-annotationdbi 1.42.1 r341_0
        - bioconductor-biobase 2.40.0 r341h470a237_0
        - bioconductor-biocgenerics 0.26.0 r341_0
        - bioconductor-biocparallel 1.14.2 r341h26a2512_0
        - bioconductor-biomart 2.36.1 r341_0
        - bioconductor-biostrings 2.48.0 r341h470a237_0
        - bioconductor-bsgenome 1.48.0 r341_0
        - bioconductor-delayedarray 0.6.6 r341_0
        - bioconductor-genomeinfodb 1.16.0 r341_0
        - bioconductor-genomeinfodbdata 1.1.0 r341_0
        - bioconductor-genomicalignments 1.16.0 r341h470a237_0
        - bioconductor-genomicfeatures 1.32.3 r341_0
        - bioconductor-genomicranges 1.32.7 r341h470a237_0
        - bioconductor-iranges 2.14.12 r341h470a237_0
        - bioconductor-rhtslib 1.12.1 r341ha92aebf_0
        - bioconductor-rsamtools 1.32.3 r341hfc679d8_0
        - bioconductor-rtracklayer 1.40.6 r341h470a237_0
        - bioconductor-s4vectors 0.18.3 r341h470a237_0
        - bioconductor-summarizedexperiment 1.10.1 r341_0
        - bioconductor-variantannotation 1.26.1 r341h470a237_0
        - bioconductor-xvector 0.20.0 r341h470a237_0
        - bioconductor-zlibbioc 1.26.0 r341h470a237_0
        - bzip2 1.0.6 h470a237_2
        - ca-certificates 2018.10.15 ha4d7672_0
        - cairo 1.14.12 h276e583_5
        - curl 7.61.0 h93b3f91_2
        - fontconfig 2.13.1 h65d0f4c_0
        - freetype 2.9.1 h6debe1e_4
        - gettext 0.19.8.1 h5e8e0c9_1
        - glib 2.56.2 h464dc38_0
        - graphite2 1.3.12 hfc679d8_1
        - gsl 2.2.1 h0c605f7_3
        - harfbuzz 1.9.0 h04dbb29_1
        - icu 58.2 hfc679d8_0
        - jpeg 9c h470a237_1
        - krb5 1.14.6 0
        - libffi 3.2.1 hfc679d8_5
        - libgcc-ng 7.2.0 hdf63c60_3
        - libgfortran 3.0.0 1
        - libiconv 1.15 h470a237_3
        - libpng 1.6.35 ha92aebf_2
        - libssh2 1.8.0 h5b517e9_2
        - libstdcxx-ng 7.2.0 hdf63c60_3
        - libtiff 4.0.9 he6b73bb_2
        - libuuid 2.32.1 h470a237_2
        - libxcb 1.13 h470a237_2
        - libxml2 2.9.8 h422b904_5
        - ncurses 6.1 hfc679d8_1
        - openssl 1.0.2p h470a237_1
        - pango 1.40.14 he752989_2
        - pcre 8.41 hfc679d8_3
        - pixman 0.34.0 h470a237_3
        - pthread-stubs 0.4 h470a237_1
        - r-assertthat 0.2.0 r341h6115d3f_1
        - r-base 3.4.1 h4fe35fd_8
        - r-bh 1.66.0_1 r341_1
        - r-bit 1.1_12 r341h470a237_2
        - r-bit64 0.9_7 r341hc070d10_0
        - r-bitops 1.0_6 r341hc070d10_2
        - r-blob 1.1.1 r341_1
        - r-crayon 1.3.4 r341h6115d3f_1
        - r-curl 3.2 r341hc070d10_2
        - r-dbi 1.0.0 r341h6115d3f_1
        - r-digest 0.6.18 r341hc070d10_0
        - r-formatr 1.5 r341h6115d3f_1
        - r-futile.logger 1.4.3 r341h6115d3f_1
        - r-futile.options 1.0.1 r341h6115d3f_0
        - r-glue 1.3.0 r341h470a237_2
        - r-hms 0.4.2 r341h6115d3f_0
        - r-httr 1.3.1 r341h6115d3f_1
        - r-jsonlite 1.5 r341hc070d10_2
        - r-lambda.r 1.2.3 r341h6115d3f_0
        - r-lattice 0.20_35 r341hc070d10_0
        - r-magrittr 1.5 r341h6115d3f_1
        - r-matrix 1.2_14 r341hc070d10_2
        - r-matrixstats 0.54.0 r341hc070d10_0
        - r-memoise 1.1.0 r341h6115d3f_1
        - r-mime 0.5 r341hc070d10_2
        - r-openssl 1.0.2 r341h9f97512_0
        - r-pkgconfig 2.0.2 r341h6115d3f_1
        - r-plogr 0.2.0 r341h6115d3f_1
        - r-prettyunits 1.0.2 r341h6115d3f_1
        - r-progress 1.2.0 r341h6115d3f_2
        - r-r6 2.2.2 r341h6115d3f_1
        - r-rcpp 0.12.17 r341h9d2a408_2
        - r-rcurl 1.95_4.11 r341h86b9717_2
        - r-rlang 0.3.0 r341h470a237_0
        - r-rsqlite 2.1.1 r341h9d2a408_0
        - r-snow 0.4_3 r341h6115d3f_0
        - r-stringi 1.2.4 r341h9d2a408_1
        - r-stringr 1.3.1 r341h6115d3f_1
        - r-vgam 1.0_6 r341h364d78e_0
        - r-xml 3.98_1.16 r341hc070d10_0
        - readline 7.0 haf1bffa_1
        - tk 8.6.8 ha92aebf_0
        - wget 1.19.5 h1ad7b7a_0
        - xorg-kbproto 1.0.7 h470a237_2
        - xorg-libice 1.0.9 h470a237_4
        - xorg-libsm 1.2.3 h8c8a85c_0
        - xorg-libx11 1.6.6 h470a237_0
        - xorg-libxau 1.0.8 h470a237_6
        - xorg-libxdmcp 1.1.2 h470a237_7
        - xorg-libxext 1.3.3 h470a237_4
        - xorg-libxrender 0.9.10 h470a237_2
        - xorg-libxt 1.1.5 h470a237_2
        - xorg-renderproto 0.11.1 h470a237_2
        - xorg-xextproto 7.3.0 h470a237_2
        - xorg-xproto 7.0.31 h470a237_7
        - xz 5.2.4 h470a237_1
        - zlib 1.2.11 h470a237_3
    run:
        - bioconductor-biostrings >=2.48.0,<2.50.0
        - bioconductor-genomicranges >=1.32.7,<1.34.0
        - bioconductor-iranges >=2.14.12,<2.16.0
        - bioconductor-rhtslib >=1.12.1,<1.14.0
        - bioconductor-summarizedexperiment >=1.10.1,<1.12.0
        - bioconductor-variantannotation >=1.26.1,<1.28.0
        - libgcc-ng >=4.9
        - libstdcxx-ng >=4.9
        - r-base >=3.4.1,<3.4.2.0a0
        - r-vgam
test:
    commands:
        - $R -e "library('deepSNV')"
about:
    home: http://bioconductor.org/packages/3.7/bioc/html/deepSNV.html
    license: GPL-3
    summary: 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.
extra:
    copy_test_source_files: true
    final: true
    identifiers:
        - biotools:deepsnv
