ascat: init

5 files changed, 352 insertions, 0 deletions

diff --git a/default.nix b/default.nix
index 4f16640..aa3d8d2 100644
--- a/default.nix
+++ b/default.nix
@@ -30,6 +30,7 @@ let
     samtools = callBionix ./tools/samtools.nix {};
     snpeff = callBionix ./tools/snpeff.nix {};
     strelka = callBionix ./tools/strelka.nix {};
+    ascat = callBionix ./tools/ascat.nix {};
 
     qsub = attrs: bionix.extend (self: super: with self; rec {
       qsubDefs = { ppn = 1; mem = 1; walltime = "24:00:00"; tmpDir = "/tmp"; sleepTime = 60; queue = null; qsubFlags = null; } // attrs;
diff --git a/tools/ascat-app.nix b/tools/ascat-app.nix
new file mode 100644
index 0000000..51aa677
--- /dev/null
+++ b/tools/ascat-app.nix
@@ -0,0 +1,269 @@
+{stdenv, callPackage, buildPerlPackage, fetchurl, fetchFromGitHub, perlPackages, R, bwa, samtools, pkgconfig, zlib, htslib, curl, bzip2, lzma, gnutls, nettle, gmp, p11-kit, libtasn1, perl, psmisc, time, vcftools, rWrapper, rPackages}:
+
+let
+  ascat = fetchurl {
+    url = "https://raw.githubusercontent.com/Crick-CancerGenomics/ascat/v2.5.1/ASCAT/R/ascat.R";
+    sha256 = "1rja9s6rksmi0kc6lhx1vr5yqv2xazgxdlwc7mbj2m881x8nngb1";
+  };
+
+  libmaus2 = stdenv.mkDerivation rec {
+    name = "libmaus-${version}";
+    version = "2.0.499-release-20180606122508";
+    src = fetchFromGitHub {
+      owner = "gt1";
+      repo = "libmaus2";
+      rev = version;
+      sha256 = "1rk2f3jirn84vgsfml4c8pr6vl5s0xbds1d0givb5pvjmc6jz61x";
+    };
+    buildInputs = [ zlib ];
+  };
+
+  biobambam2 = stdenv.mkDerivation rec {
+    name = "biobambam-${version}";
+    version = "2.0.87-release-20180301132713";
+    src = fetchFromGitHub {
+      owner = "gt1";
+      repo = "biobambam2";
+      rev = version;
+      sha256 = "1hjh6kl62hr9afi6fa6x563823lmmmijh1y2204db0nfnaybnrn6";
+    };
+    nativeBuildInputs = [ pkgconfig ];
+    buildInputs = [ libmaus2 zlib ];
+  };
+
+  libBigWig = stdenv.mkDerivation rec {
+    name = "libBigWig-${version}";
+    version = "0.4.2";
+    src = fetchFromGitHub {
+      owner = "dpryan79";
+      repo = "libBigWig";
+      rev = version;
+      sha256 = "0h2smg24v5srdcqzrmz2g23cmlp4va465mgx8r2z571sfz8pv454";
+    };
+    buildInputs = [ curl ];
+    makeFlags = [ "prefix=$(out)" ];
+  };
+
+  cgpBigWig = stdenv.mkDerivation rec {
+    name = "cgpBigWig-${version}";
+    version = "1.0.2";
+    src = fetchFromGitHub {
+      owner = "cancerit";
+      repo = "cgpBigWig";
+      rev = version;
+      sha256 = "1piprbibmrwbh524plp9s35z5cf1yk7713dxsdik2qv363p6pfsa";
+    };
+    buildInputs = [ htslib libBigWig curl bzip2 lzma gnutls libtasn1 nettle gmp p11-kit ];
+    configurePhase = ''
+      cd c
+      patchShebangs .
+    '';
+    makeFlags = [ "HTSLIB=${htslib}" "LIBBIGWIG=${libBigWig}" ];
+    installPhase = ''
+      mkdir -p $out
+      cp -r ../bin $out
+    '';
+  };
+
+  BioDBHTS = buildPerlPackage rec {
+    name = "Bio-DB-HTS-${version}";
+    version = "2.11";
+    src = fetchFromGitHub {
+      owner = "Ensembl";
+      repo = "Bio-DB-HTS";
+      rev = version;
+      sha256 = "0n60vmsd39pz6zbkwz78fdzsmfg8dxgwx0m166vm8515q446922c";
+    };
+    nativeBuildInputs = with perlPackages; [ ModuleBuild ];
+    buildInputs = [ htslib zlib ];
+    #propagatedBuildInputs = [ BioRootVersion ];
+    configurePhase = ''
+      export HTSLIB_DIR=${htslib}
+      sed -i 's|"-Wl,-rpath,\$hts_lib",||' Build.PL
+      perl ./Build.PL --install_base=$out
+    '';
+    buildPhase = ''
+      ./Build
+    '';
+    installPhase = ''
+      ./Build install
+      mkdir -p $out/lib/perl5/site_perl/${perl.version}
+      mv $out/lib/perl5/x86_64-linux-thread-multi $out/lib/perl5/site_perl/${perl.version}
+    '';
+  };
+
+  BioPerl = buildPerlPackage rec {
+    name = "BioPerl-1.7.4";
+    src = fetchurl {
+      url = "mirror://cpan/authors/id/C/CD/CDRAUG/${name}.tar.gz";
+      sha256 = "0yvhgifs8g9rwdcq84zw4b005nq2jml6c75zgjscv6d2pd3lj1ss";
+    };
+    propagatedBuildInputs = with perlPackages; [DBI DataStag Error GD Graph HTTPMessage HTTPMessage IOstringy IOString IPCRun LWP ListMoreUtils SetScalar TestMost TestRequiresInternet URI XMLDOM XMLDOMXPath XMLLibXML XMLLibXML libxml_perl XMLSAX XMLSAXBase XMLSAXWriter XMLTwig XMLWriter YAML DBFile ];
+    nativeBuildInputs = with perlPackages; [ TestException TestWarn TestDifferences TestDeep ];
+  };
+
+  DataStag = buildPerlPackage rec {
+    name = "Data-Stag-0.14";
+    src = fetchurl {
+      url = "mirror://cpan/authors/id/C/CM/CMUNGALL/${name}.tar.gz";
+      sha256 = "0ncf4l39ka23nb01jlm6rzxdb5pqbip01x0m38bnvf1gim825caa";
+    };
+    propagatedBuildInputs = with perlPackages; [IOString Graph XMLLibXSLT ];
+  };
+
+  XMLDOMXPath = buildPerlPackage rec {
+    name = "XML-DOM-XPath-0.14";
+    src = fetchurl {
+      url = "mirror://cpan/authors/id/M/MI/MIROD/${name}.tar.gz";
+      sha256 = "1si9m1pqih3ibbd6jnw69fh98dd4krxpx90p65x9j4aja55afwq1";
+    };
+    propagatedBuildInputs= with perlPackages; [XMLDOM XMLXPathEngine];
+    doCheck = false;
+  };
+
+  pcapCore = buildPerlPackage rec {
+    name = "PCAP-core-${version}";
+    version = "4.2.3";
+    src = fetchFromGitHub {
+      owner = "cancerit";
+      repo = "PCAP-core";
+      rev = version;
+      sha256 = "0ia9z0k4jpa02596smivpkw85vi9sv7sbxnysv7jdyh2g1rv1s5c";
+    };
+    nativeBuildInputs = with perlPackages; [ TestFatal TestWarn ];
+    propagatedBuildInputs = with perlPackages; [
+      bwa
+      samtools
+      biobambam2
+      cgpBigWig
+      ConstFast
+      FileWhich
+      IPCSystemSimple
+      CaptureTiny
+      TermUI
+      BioDBHTS
+      DataUUID
+      YAML
+      BioPerl
+      JSON
+      psmisc
+    ];
+    preConfigure = ''
+      sed -i 's|/usr/bin/time|${time}/bin/time|' lib/PCAP/Threaded.pm
+      sed -i 's|/bin/bash|${stdenv.shell}|' lib/PCAP/Threaded.pm
+    '';
+  };
+
+  cgpVcf = buildPerlPackage rec {
+    name = "cgpVCF-${version}";
+    version = "2.0.4";
+    outputs = [ "out" "dev" ];
+    src = fetchFromGitHub {
+      owner = "cancerit";
+      repo = "cgpVcf";
+      rev = "v${version}";
+      sha256 = "0j8spk02v4l0nrqsa42d57djb4nm71daz5hvlm5fwakfq8037yx4";
+    };
+    nativeBuildInputs = with perlPackages; [ TestFatal TestWarn ];
+    propagatedBuildInputs = with perlPackages; [
+      ConstFast
+      samtools
+      vcftools
+      DataUUID
+      DateTime
+      IPCSystemSimple
+    ];
+  };
+
+  BDebug = buildPerlPackage rec {
+    name = "B-Debug-1.26";
+    src = fetchurl {
+      url = "mirror://cpan/authors/id/R/RU/RURBAN/${name}.tar.gz";
+      sha256 = "0fhdaxpkirgnwivd0a7x83dvfwqbngsq2rcfwvfxipgh6i8kyvcd";
+    };
+  };
+
+  DevelCover = buildPerlPackage rec {
+    name = "Devel-Cover-1.31";
+    src = fetchurl {
+      url = "mirror://cpan/authors/id/P/PJ/PJCJ/${name}.tar.gz";
+      sha256 = "0wsd7fkpy5qwnz68hz624frnbqii5igg6l2q7n1mx1lh32vn0kcr";
+    };
+    nativeBuildInputs = with perlPackages; [ BDebug ];
+    doCheck = false;
+  };
+
+
+  alleleCount = stdenv.mkDerivation rec {
+    name = "alleleCount-${version}";
+    version = "4.0.1";
+    src = fetchFromGitHub {
+      owner = "cancerit";
+      repo = "alleleCount";
+      rev = "v${version}";
+      sha256 = "0nkwnjqglgshzhlmz1r0khdjai9mfz4ih8bzrzg0g18d1725k6gp";
+    };
+    buildInputs = [ htslib perl zlib bzip2 lzma ];
+    preConfigure = "cd c";
+    installPhase = ''
+      mkdir -p $out/bin
+      cp bin/* $out/bin
+    '';
+  };
+
+  alleleCountPerl = buildPerlPackage rec {
+    name = "alleleCount.pl-${version}";
+    version = "4.0.1";
+    src = fetchFromGitHub {
+    owner = "cancerit";
+    repo = "alleleCount";
+    rev = "v${version}";
+    sha256 = "0nkwnjqglgshzhlmz1r0khdjai9mfz4ih8bzrzg0g18d1725k6gp";
+    };
+    preConfigure = ''
+      cd perl
+    '';
+    nativeBuildInputs = with perlPackages; [
+      TestFatal
+    ];
+    propagatedBuildInputs = with perlPackages; [
+      ConstFast
+      DevelCover
+      FileSlurp
+      FileWhich
+      PodCoverage
+      TryTiny
+      alleleCount
+      IPCSystemSimple
+    ];
+  };
+
+  ascatR = rWrapper.overrideAttrs (attrs: {
+    packages = with rPackages; [ RColorBrewer ];
+  });
+
+  ascatNGS = buildPerlPackage rec {
+    name = "ascatNGS-${version}";
+    version = "4.1.2";
+    src = fetchFromGitHub {
+      owner = "cancerit";
+      repo = "ascatNgs";
+      rev = "v${version}";
+      sha256 = "0qc1wp37k2c9vya992cfiphp2jpp8hvfvqz5ydi2d5b71prfaw82";
+    };
+    preConfigure = ''
+      cd perl
+      cp ${ascat} share/ascat/ascat.R
+    '';
+    nativeBuildInputs = with perlPackages; [ TestFatal TestWarn ];
+    propagatedBuildInputs = with perlPackages; [
+      ascatR
+      FileShareDirInstall
+      pcapCore
+      FileShareDir
+      cgpVcf
+      alleleCountPerl
+    ];
+  };
+
+in ascatNGS
diff --git a/tools/ascat-callCNV.nix b/tools/ascat-callCNV.nix
new file mode 100644
index 0000000..357ab8a
--- /dev/null
+++ b/tools/ascat-callCNV.nix
@@ -0,0 +1,37 @@
+{ bionix
+, ref
+, gc
+, indexAttrs ? {}
+, bamIndexAttrs ? {}
+, flags ? null
+}:
+
+{tumour, normal, gender}:
+
+with bionix;
+with lib;
+with types;
+
+stage rec {
+  name = "ascat-callCNV";
+  buildInputs = with pkgs; [ ascat.app ];
+  buildCommand = ''
+    mkdir $out
+    ln -s ${tumour} tumour.bam
+    ln -s ${bionix.samtools.index bamIndexAttrs tumour} tumour.bai
+    ln -s ${normal} normal.bam
+    ln -s ${bionix.samtools.index bamIndexAttrs normal} normal.bai
+    ln -s ${ref} ref.fa
+    ln -s ${samtools.faidx indexAttrs ref} ref.fa.fai
+    ascat.pl \
+      -outdir $out \
+      -tumour tumour.bam \
+      -normal normal.bam \
+      -reference ref.fa \
+      -snp_gc ${gc} \
+      -gender ${gender} \
+      -genderChr Y \
+      -protocol WGS \
+      -cpus $NIX_BUILD_CORES
+  '';
+}
diff --git a/tools/ascat-gccorrect.nix b/tools/ascat-gccorrect.nix
new file mode 100644
index 0000000..c1838d9
--- /dev/null
+++ b/tools/ascat-gccorrect.nix
@@ -0,0 +1,36 @@
+{ bionix
+, ref
+, chrPrefix ? ""
+, flags ? null
+}:
+
+snp:
+
+with bionix;
+with lib;
+with types;
+
+stage rec {
+  name = "ascat-gccorrect";
+  buildInputs = with pkgs; [ ascat.app gawk ];
+  script = pkgs.writeText "convert.awk" ''
+    BEGIN{
+      FS = OFS = "\t"
+    }
+    /^#/{next}
+    !loc[$1,$2]{
+      print $3, "${chrPrefix}" $1, $2
+      loc[$1,$2]++
+    }
+  '';
+  buildCommand = ''
+    awk -f ${script} ${snp} > snpPos.tsv
+    mkdir splitPos splitGc splitGcLogs
+    split --number=l/$NIX_BUILD_CORES -d snpPos.tsv splitPos/snpPos.
+    ls -1 splitPos/ | xargs -n1 -P$NIX_BUILD_CORES -I '{}' sh -c 'ascatSnpPanelGcCorrections.pl ${ref} splitPos/{} > splitGc/{}'
+    mv splitGc/snpPos.00 $out
+    for f in splitGc/* ; do
+      sed 1d $f >> $out
+    done
+  '';
+}
diff --git a/tools/ascat.nix b/tools/ascat.nix
new file mode 100644
index 0000000..05e2299
--- /dev/null
+++ b/tools/ascat.nix
@@ -0,0 +1,9 @@
+{bionix}:
+
+with bionix;
+
+{
+  app = pkgs.callPackage ./ascat-app.nix {};
+  gccorrect = callBionixE ./ascat-gccorrect.nix;
+  callCNV = callBionixE ./ascat-callCNV.nix;
+}