aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--default.nix1
-rw-r--r--tools/mutect-app.nix32
-rw-r--r--tools/mutect-call.nix42
-rw-r--r--tools/mutect.nix9
4 files changed, 84 insertions, 0 deletions
diff --git a/default.nix b/default.nix
index 2ce7b1d..5218a99 100644
--- a/default.nix
+++ b/default.nix
@@ -16,6 +16,7 @@ let
gridss = callBionix ./tools/gridss.nix {};
infercnv = callBionix ./tools/infercnv.nix {};
mosdepth = callBionix ./tools/mosdepth.nix {};
+ mutect = callBionix ./tools/mutect.nix {};
platypus = callBionix ./tools/platypus.nix {};
samtools = callBionix ./tools/samtools.nix {};
strelka = callBionix ./tools/strelka.nix {};
diff --git a/tools/mutect-app.nix b/tools/mutect-app.nix
new file mode 100644
index 0000000..02c4f51
--- /dev/null
+++ b/tools/mutect-app.nix
@@ -0,0 +1,32 @@
+{stdenv, fetchurl, makeWrapper, unzip, fetchFromGitHub}:
+
+let
+ oldnix = import (fetchFromGitHub {
+ owner = "NixOS";
+ repo = "nixpkgs";
+ rev = "83a893c38a83877588e3ca7ccfeabaa973c30acd";
+ sha256 = "0q7214hag7h95irvhkdb648m09b9jspb0raw1qjrx7y4grzb165h";
+ }) {};
+
+ jre = oldnix.openjdk7;
+
+in stdenv.mkDerivation rec {
+ name = "mutect-${version}";
+ version = "1.1.5";
+
+ src = fetchurl {
+ url = "https://github.com/broadinstitute/mutect/releases/download/${version}/muTect-${version}-bin.zip";
+ sha256 = "1pq7iv720bp970qsyyshwk98xdb7naw566y6gk9cpj6bmm08z9v3";
+ };
+
+ buildInputs = [ makeWrapper jre unzip ];
+
+ unpackPhase = ''
+ unzip $src -d $TMPDIR
+ '';
+ installPhase = ''
+ install -Dt $out/libexec/mutect muTect-${version}.jar
+ mkdir $out/bin
+ makeWrapper ${jre}/bin/java $out/bin/mutect --add-flags "-jar $out/libexec/mutect/muTect-${version}.jar"
+ '';
+}
diff --git a/tools/mutect-call.nix b/tools/mutect-call.nix
new file mode 100644
index 0000000..9fd009b
--- /dev/null
+++ b/tools/mutect-call.nix
@@ -0,0 +1,42 @@
+{bionix
+, nixpkgs
+, cosmic
+, dbsnp}:
+
+with nixpkgs;
+with lib;
+
+let
+ inherit (bionix.types) matchFiletype;
+ getVCFref = matchFiletype "mutect-call" {vcf = {ref}: ref;};
+ getBAMref = matchFiletype "mutect-call" {bam = {ref, ...}: ref;};
+ refs = map getVCFref [ cosmic dbsnp ];
+ ref = head refs;
+in
+
+assert (length (unique refs) == 1);
+
+{normal, tumour}:
+
+assert (ref == getBAMref normal && ref == getBAMref tumour);
+
+stdenv.mkDerivation {
+ name = "mutect";
+ buildInputs = [ bionix.mutect.app ];
+ buildCommand = ''
+ ln -s ${normal} normal.bam
+ ln -s ${tumour} tumour.bam
+ ln -s ${dbsnp} dbsnp.vcf
+ ln -s ${cosmic} cosmic.vcf
+ ln -s ${ref} ref.fa
+ ln -s ${bionix.samtools.faidx {} ref} ref.fa.fai
+ ln -s ${bionix.samtools.dict {} ref} ref.dict
+ mutect --analysis_type MuTect \
+ --reference_sequence ref.fa \
+ --cosmic cosmic.vcf \
+ --dbsnp dbsnp.vcf \
+ --input_file:normal normal.bam \
+ --input_file:tumour tumour.bam \
+ --out $out
+ '';
+}
diff --git a/tools/mutect.nix b/tools/mutect.nix
new file mode 100644
index 0000000..9a8ce41
--- /dev/null
+++ b/tools/mutect.nix
@@ -0,0 +1,9 @@
+{bionix, nixpkgs}:
+
+with nixpkgs;
+with bionix;
+
+{
+ app = callPackage ./mutect-app.nix {inherit (nixpkgs) stdenv fetchurl makeWrapper unzip fetchFromGitHub;};
+ call = callBionix ./mutect-call.nix;
+}