lib/references.nix


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{ bionix, nixpkgs }:

with nixpkgs;
with bionix.types;

rec {
  grch38 = grch38-p12;
  grch38-p12 = {
    seq = stdenvNoCC.mkDerivation rec {
      name = "seq-grch38.${version}";
      version = "p12";
      src = fetchurl {
        url = "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/GRCh38.p12.genome.fa.gz";
        sha256 = "0ji2ggpmgnbpwbhq8mirj6h3lyy02nl2rnz7n892iq5cqpsblh4z";
      };
      buildCommand = "gunzip < $src > $out";
      passthru.filetype = filetype.fa {};
    };
    blacklist = stdenvNoCC.mkDerivation {
      name = "blacklist-grch38";
      src = fetchurl {
        url = "http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz";
        sha256 = "1lpnqq1mjidbdxj5i6x26rxa8x1rs8q3hlf0z1z49j3jsnkgffky";
      };
      buildCommand = "gunzip < $src > $out";
      passthru.filetype = filetype.bed { ref = seq; };
    };
  };

  grcm38 = grcm38-p6;
  grcm38-p6 = {
    seq = stdenvNoCC.mkDerivation rec {
      name = "seq-grcm38.${version}";
      version = "p6";
      src = fetchurl {
        url = "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M19/GRCm38.${version}.genome.fa.gz";
        sha256 = "0ryiqab5bldpzawylsk2qpjxr2j701q03ww9jqyxhkimqpn9g3mr";
      };
      buildCommand = "gunzip < $src > $out";
      passthru.filetype = filetype.fa {};
    };
  };

  mm10 = mm10-p4;
  mm10-p4 = {
      seq = stdenvNoCC.mkDerivation rec {
          name = "seq-mm10.${version}";
          version = "p4";
          src = fetchurl {
              url = "http://hgdownload.soe.ucsc.edu/goldenPath/mm10/mm10Patch4/mm10Patch4.fa.gz";
              sha256 = "1660d6d05f3aa266c6053cfd1efef1747d9e854836917241d6f47cff7a55340c";
              };
          buildCommand = "gunzip < $src > $out";
          passthru.filetype = filetype.fa {};
      };
  };
}