From 8a2778f8853ab687f83e07c4c322ab843b08f2af Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 22 Apr 2020 20:44:43 +1000
Subject: whisper: init 2.0

---
 default.nix             |  1 +
 test-tnpair.nix         |  3 ++-
 tools/whisper-align.nix | 39 +++++++++++++++++++++++++++++++++++++++
 tools/whisper-index.nix | 21 +++++++++++++++++++++
 tools/whisper.nix       |  9 +++++++++
 5 files changed, 72 insertions(+), 1 deletion(-)
 create mode 100644 tools/whisper-align.nix
 create mode 100644 tools/whisper-index.nix
 create mode 100644 tools/whisper.nix

diff --git a/default.nix b/default.nix
index 98b2e5a..170a6d3 100644
--- a/default.nix
+++ b/default.nix
@@ -46,6 +46,7 @@ let
     delly = callBionix ./tools/delly.nix {};
     lumpy = callBionix ./tools/lumpy.nix {};
     lastal = callBionix ./tools/last.nix {};
+    whisper = callBionix ./tools/whisper.nix {};
 
     slurm = attrs: bionix.extend (self: super: with self; rec {
       slurmDefs = { ppn = 1; mem = 1; walltime = "24:00:00"; partition = null; slurmFlags = null; salloc = "/usr/bin/salloc"; srun = "/usr/bin/srun"; } // attrs;
diff --git a/test-tnpair.nix b/test-tnpair.nix
index 38e3333..cc493fc 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -54,6 +54,7 @@ let
   alignments = {
     "bowtie-normal.bam" = bowtie.align {inherit ref;} tnpair.normal.files;
     "last.maf" = lastal.align {inherit ref;} tnpair.normal.files;
+    "whisper.bam" = whisper.align {inherit ref;} tnpair.normal.files;
     "bwa-mem.bam" = bwa.mem {inherit ref;} tnpair.normal.files;
     "bwa-mem2.bam" = bwa.mem2 {inherit ref;} tnpair.normal.files;
     "minimap2-normal.bam" = minimap2.align {inherit ref; preset = "sr"; } tnpair.normal.files;
@@ -92,4 +93,4 @@ let
     inherit alignments;
   };
 
-in testNaming
+in alignments."bwa-mem.bam"#testNaming
diff --git a/tools/whisper-align.nix b/tools/whisper-align.nix
new file mode 100644
index 0000000..5620fe3
--- /dev/null
+++ b/tools/whisper-align.nix
@@ -0,0 +1,39 @@
+{ bionix
+, ref
+, bamOutput ? true
+, flags ? null
+, indexAttrs ? {}
+}:
+
+{ input1
+, input2 ? null
+}:
+
+with bionix;
+with lib;
+with types;
+with compression;
+
+let
+  fa = f: matchFiletype "whisper-ref" { fa = _: f; } f;
+  fq = f: matchFiletype "whisper-input" { fq = _: f; gz = matchFiletype' "whisper-input" { fq = _: f; }; } f;
+
+in stage {
+  name = "whisper-mem";
+  buildInputs = [ whisper.app ];
+  buildCommand = ''
+    ln -s ${fa ref} ref.fa
+    for f in ${bionix.whisper.index indexAttrs ref}/* ; do
+      ln -s $f
+    done
+    whisper ${optionalString (flags != null) flags} -t $NIX_BUILD_CORES \
+      ${optionalString bamOutput "-store-BAM"} \
+      ${optionalString (input2 != null) "-rp"} \
+      -stdout \
+      index ${fq input1} \
+      ${optionalString (input2 != null) (fq input2)} \
+      > $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/whisper-index.nix b/tools/whisper-index.nix
new file mode 100644
index 0000000..675af7d
--- /dev/null
+++ b/tools/whisper-index.nix
@@ -0,0 +1,21 @@
+{ bionix
+, flags ? null
+}:
+
+ref:
+
+with bionix;
+with lib;
+with types;
+
+assert (matchFiletype "whisper-index" { fa = _: true; } ref);
+
+stage {
+  name = "whisper-index";
+  buildInputs = [ whisper.app ];
+  buildCommand = ''
+    ln -s ${ref} ref.fa
+    mkdir $out
+    whisper-index ${optionalString (flags != null) flags} index ref.fa $out $TMPDIR
+  '';
+}
diff --git a/tools/whisper.nix b/tools/whisper.nix
new file mode 100644
index 0000000..244a410
--- /dev/null
+++ b/tools/whisper.nix
@@ -0,0 +1,9 @@
+{ bionix }:
+
+with bionix;
+
+rec {
+  app = pkgs.callPackage ./whisper-app.nix {};
+  index = callBionixE ./whisper-index.nix;
+  align = callBionixE ./whisper-align.nix;
+}
-- 
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