refactor reference location to lib

1 files changed, 53 insertions, 0 deletions

diff --git a/lib/references.nix b/lib/references.nix
new file mode 100755
index 0000000..72c1243
--- /dev/null
+++ b/lib/references.nix
@@ -0,0 +1,53 @@
+{ bionix, nixpkgs }:
+
+with nixpkgs;
+
+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";
+      };
+    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 > $out";
+    };
+  };
+
+  grcm38 = grcm38-p6;
+  grcm38-p6 = {
+    seq = stdenvNoCC.mkDerivation rec {
+        name = "seq-grch38.${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 > $out";
+      };
+    };
+  };
+
+  mm10 = mm10-p4;
+  mm10-p4 = {
+      seq = stdenvNoCC.mkDerivation rec {
+          name = "seq-mm10.${version}";
+          version = "p4";
+          src = fetchurl {
+              url = "ftp://hgdownload.soe.ucsc.edu/goldenPath/mm10/mm10Patch4/mm10Patch4.fa.gz";
+              sha256 = "1660d6d05f3aa266c6053cfd1efef1747d9e854836917241d6f47cff7a55340c";
+              };
+          buildCommand = "gunzip < $src > $out";
+      };
+  };
+}