From d05214694d6784fe39e34ebfbc45202c71917d44 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 3 Oct 2018 12:57:12 +1000
Subject: refactor reference location to lib

---
 default.nix        |  2 +-
 lib/references.nix | 53 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 references.nix     | 53 -----------------------------------------------------
 3 files changed, 54 insertions(+), 54 deletions(-)
 create mode 100755 lib/references.nix
 delete mode 100755 references.nix

diff --git a/default.nix b/default.nix
index 7ba7a1e..10d2249 100644
--- a/default.nix
+++ b/default.nix
@@ -10,10 +10,10 @@ let
       gridss = callBionix ./tools/gridss.nix;
       mosdepth = callBionix ./tools/mosdepth.nix;
       platypus = callBionix ./tools/platypus.nix;
-      ref = callBionix ./references.nix;
       samtools = callBionix ./tools/samtools.nix;
       strelka = callBionix ./tools/strelka.nix;
 
       qsub = nixpkgs.callPackage ./lib/qsub.nix {};
+      ref = callBionix ./lib/references.nix;
   });
 in bionix
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 > $out";
+      };
+  };
+}
diff --git a/references.nix b/references.nix
deleted file mode 100755
index 72c1243..0000000
--- a/references.nix
+++ /dev/null
@@ -1,53 +0,0 @@
-{ bionix, nixpkgs }:
-
-with nixpkgs;
-
-rec {
-  grch38 = grch38-p12;
-  grch38-p12 = {
-    seq = stdenvNoCC.mkDerivation rec {
-        name = "seq-grch38.${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";
-      };
-  };
-}
-- 
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