Merge pull request #75843 from jbedo/lumpy

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Doron Behar 2020-10-15 19:46:13 +03:00 committed by GitHub
commit 1db3202722
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4 changed files with 110 additions and 0 deletions

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@ -0,0 +1,47 @@
{ stdenv, fetchFromGitHub, htslib, zlib, curl, openssl, samblaster, sambamba
, samtools, hexdump, python2Packages, which }:
let
python =
python2Packages.python.withPackages (pkgs: with pkgs; [ pysam numpy ]);
in stdenv.mkDerivation rec {
pname = "lumpy";
version = "0.3.0";
src = fetchFromGitHub {
owner = "arq5x";
repo = "lumpy-sv";
rev = version;
sha256 = "0azhzvmh9az9jcq0xprlzdz6w16azgszv4kshb903bwbnqirmk18";
};
nativeBuildInputs = [ which ];
buildInputs =
[ htslib zlib curl openssl python samblaster sambamba samtools hexdump ];
preConfigure = ''
patchShebangs ./.
# Use Nix htslib over bundled version
sed -i 's/lumpy_filter: htslib/lumpy_filter:/' Makefile
sed -i 's|../../lib/htslib/libhts.a|-lhts|' src/filter/Makefile
'';
# Upstream's makefile doesn't have an install target
installPhase = ''
mkdir -p $out
cp -r bin $out
cp -r scripts $out
sed -i 's|/build/source|'$out'|' $out/bin/lumpyexpress.config
'';
meta = with stdenv.lib; {
description = "Probabilistic structural variant caller";
homepage = "https://github.com/arq5x/lumpy-sv";
maintainers = with maintainers; [ jbedo ];
license = licenses.mit;
platforms = [ "x86_64-linux" ];
};
}

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@ -0,0 +1,31 @@
{ stdenv, fetchFromGitHub, python3, which, dmd, ldc, zlib }:
stdenv.mkDerivation rec {
pname = "sambamba";
version = "0.7.1";
src = fetchFromGitHub {
owner = "biod";
repo = "sambamba";
rev = "v${version}";
sha256 = "0k5wy06zrbsc40x6answgz7rz2phadyqwlhi9nqxbfqanbg9kq20";
fetchSubmodules = true;
};
nativeBuildInputs = [ which python3 dmd ldc ];
buildInputs = [ zlib ];
# Upstream's install target is broken; copy manually
installPhase = ''
mkdir -p $out/bin
cp bin/sambamba-${version} $out/bin/sambamba
'';
meta = with stdenv.lib; {
description = "SAM/BAM processing tool";
homepage = "https://lomereiter.github.io/sambamba/";
maintainers = with maintainers; [ jbedo ];
license = with licenses; gpl2;
platforms = platforms.x86_64;
};
}

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@ -0,0 +1,26 @@
{ stdenv, fetchFromGitHub }:
stdenv.mkDerivation rec {
pname = "samblaster";
version = "0.1.24";
src = fetchFromGitHub {
owner = "GregoryFaust";
repo = "samblaster";
rev = "v.${version}";
sha256 = "0iv2ddfw8363vb2x8gr3p8g88whb6mb9m0pf71i2cqsbv6jghap7";
};
installPhase = ''
mkdir -p $out/bin
cp samblaster $out/bin
'';
meta = with stdenv.lib; {
description = "Tool for marking duplicates and extracting discordant/split reads from SAM/BAM files";
maintainers = with maintainers; [ jbedo ];
license = licenses.mit;
homepage = "https://github.com/GregoryFaust/samblaster";
platforms = platforms.x86_64;
};
}

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@ -26025,6 +26025,8 @@ in
last = callPackage ../applications/science/biology/last { };
lumpy = callPackage ../applications/science/biology/lumpy { };
macse = callPackage ../applications/science/biology/macse { };
migrate = callPackage ../applications/science/biology/migrate { };
@ -26101,6 +26103,10 @@ in
mpi = true;
});
sambamba = callPackage ../applications/science/biology/sambamba { };
samblaster = callPackage ../applications/science/biology/samblaster { };
samtools = callPackage ../applications/science/biology/samtools { };
samtools_0_1_19 = callPackage ../applications/science/biology/samtools/samtools_0_1_19.nix {
stdenv = gccStdenv;