4 files changed, 95 insertions, 0 deletions
diff --git a/tools/snap-align.nix b/tools/snap-align.nix
new file mode 100644
index 0000000..4647142
--- /dev/null
+++ b/tools/snap-align.nix
@@ -0,0 +1,37 @@
+{ bionix
+, ref
+, bamOutput ? true
+, flags ? null
+, indexAttrs ? {}
+}:
+
+{ input1
+, input2 ? null
+}:
+
+with bionix;
+with lib;
+with types;
+with compression;
+
+let
+  fa = f: matchFiletype "snap-ref" { fa = _: f; } f;
+  fq = f: matchFiletype "snap-input" { fq = _: f; gz = matchFiletype' "snap-input" { fq = _: f; }; } f;
+
+in stage {
+  name = "snap-align";
+  buildInputs = with pkgs; [ bionix.snap.app bc ] ++ optional bamOutput samtools;
+  buildCommand = ''
+    for f in /* ; do
+      ln -s $f
+    done
+    snap-aligner ${if input2 == null then "single" else "paired"} ${bionix.snap.index indexAttrs ref} ${fq input1} \
+      ${optionalString (input2 != null) (fq input2)} \
+      -o ${if bamOutput then "-bam" else "-sam" } - \
+      -t $NIX_BUILD_CORES \
+      ${optionalString (flags != null) flags} \
+      | samtools sort -n > $out
+  '';
+  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.multicore = true;
+}
diff --git a/tools/snap-app.nix b/tools/snap-app.nix
new file mode 100644
index 0000000..c845d1f
--- /dev/null
+++ b/tools/snap-app.nix
@@ -0,0 +1,19 @@
+{stdenv, fetchFromGitHub, zlib}:
+
+stdenv.mkDerivation rec {
+  name = "snap-git";
+  src = fetchFromGitHub {
+    owner = "amplab";
+    repo = "snap";
+    rev = "669a341cfa5c3e0a80098bf5aa51e3332f868d2b";
+    sha256 = "1810d8wn88wbagip7hlnwwg7z6jqyiyfnnvdiir06s3rrmn95mjh";
+  };
+  buildInputs = [ zlib ];
+  postConfigure = ''
+    sed -i 's/-Wno-format/-Wformat/g' Makefile
+  '';
+  installPhase = ''
+    mkdir -p $out/bin
+    cp snap-aligner $out/bin
+  '';
+}
diff --git a/tools/snap-index.nix b/tools/snap-index.nix
new file mode 100644
index 0000000..b72ee01
--- /dev/null
+++ b/tools/snap-index.nix
@@ -0,0 +1,22 @@
+{ bionix
+, flags ? null
+}:
+
+ref:
+
+with bionix;
+with lib;
+with types;
+
+assert (matchFiletype "snap-index" { fa = _: true; } ref);
+
+stage {
+  name = "snap-index";
+  buildInputs = [ bionix.snap.app ];
+  buildCommand = ''
+    ln -s ${ref} ref.fa
+    mkdir $out
+    snap-aligner index ref.fa $out -t$NIX_BUILD_CORES ${optionalString (flags != null) flags}
+  '';
+  passthru.multicore = true;
+}
diff --git a/tools/snap.nix b/tools/snap.nix
new file mode 100644
index 0000000..851c51a
--- /dev/null
+++ b/tools/snap.nix
@@ -0,0 +1,17 @@
+{ bionix }:
+
+with bionix;
+
+rec {
+  app = pkgs.callPackage ./snap-app.nix {};
+
+  /* Align reads against a reference
+  Type: snap :: {ref :: fasta, bamOutput :: bool, ...} -> {input1, input2} -> bam/sam
+  */
+  align = callBionixE ./snap-align.nix;
+
+  /* Creates an reference index for SNAP
+  Type: index :: {...} -> fasta -> SNAP index
+  */
+  index = callBionixE ./snap-index.nix;
+}