genmap: init

1 files changed, 22 insertions, 0 deletions

diff --git a/tools/genmap-calcmap.nix b/tools/genmap-calcmap.nix
new file mode 100644
index 0000000..df9ccc3
--- /dev/null
+++ b/tools/genmap-calcmap.nix
@@ -0,0 +1,22 @@
+{ bionix
+, k ? 30
+, e ? 2
+}:
+
+with bionix;
+
+ref: stage {
+  name = "genmap-mappability";
+  buildInputs = with pkgs; [ genmap ];
+  buildCommand = ''
+    mkdir $out
+    genmap map \
+      -K ${toString k} \
+      -E ${toString e} \
+      --wig \
+      -I ${bionix.genmap.index {} ref} \
+      -O $out \
+      -T $NIX_BUILD_CORES
+  '';
+  passthru.multicore = true;
+}