80 lines
2.0 KiB
Nix
80 lines
2.0 KiB
Nix
{ stdenv, lib, fetchFromGitHub, which, autoconf, automake
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, zlib, curl
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, python2, fetchPypi, hexdump, sambamba, samblaster, samtools }: let
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python = python2.override {
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packageOverrides = final: prev: {
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numpy = prev.numpy.overridePythonAttrs(old: rec {
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version = "1.16.6";
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disabled = false;
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src = fetchPypi {
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inherit version;
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pname = "numpy";
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extension = "zip";
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sha256 = "e5cf3fdf13401885e8eea8170624ec96225e2174eb0c611c6f26dd33b489e3ff";
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};
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nativeCheckInputs = [
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prev.pytest
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# "hypothesis" indirectly depends on numpy to build its documentation.
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prev.hypothesis
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prev.typing-extensions
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];
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});
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};
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};
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in stdenv.mkDerivation rec {
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version = "0.3.0";
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name = "lumpy-${version}";
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src = fetchFromGitHub {
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inherit name;
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owner = "arq5x";
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repo = "lumpy-sv";
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rev = version;
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fetchSubmodules = true;
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sha256 = "1r6sssbnz017jpnsfb6dfjj0y7bzxgxxdikz4rak569m6kqkawqq";
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};
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installPhase = ''
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mkdir -p "$out"
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cp -r bin "$out"
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substituteInPlace "$out/bin/lumpyexpress.config" \
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--replace "$PWD/" "$out"
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mkdir -p "$out/lib/lumpy/bamkit"
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for script in \
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pairend_distro.py \
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bamkit/bamgroupreads.py \
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bamkit/bamfilterrg.py \
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bamkit/bamlibs.py
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do
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cp "scripts/$script" "$out/lib/lumpy/$script"
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substituteInPlace "$out/bin/lumpyexpress.config" \
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--replace "$out/scripts/$script" "$out/lib/lumpy/$script"
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done
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'';
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buildInputs = [
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which
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autoconf
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automake
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zlib
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curl
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(python.withPackages (packages: with packages;
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[
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numpy
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pysam
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]
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))
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hexdump
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sambamba
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samblaster
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samtools
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];
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meta = with lib; {
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description = "A probabilistic framework for structural variant discovery.";
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homepage = https://github.com/arq5x/lumpy-sv;
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platforms = platforms.all;
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license = licenses.mit;
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};
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}
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