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manta: init 1.6.0

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Justin Bedo 2019-12-16 16:31:09 +11:00 committed by Jon
parent d4119389bd
commit 7f142260d3
2 changed files with 37 additions and 0 deletions
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35
pkgs/applications/science/biology/manta/default.nix Normal file
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@ -0,0 +1,35 @@
{ stdenv, fetchFromGitHub, cmake, zlib, python2 }:
stdenv.mkDerivation rec {
pname = "manta";
version = "1.6.0";
src = fetchFromGitHub {
owner = "Illumina";
repo = "manta";
rev = "v${version}";
sha256 = "1711xkcw8rpw9xv3bbm7v1aryjz4r341rkq5255192dg38sgq7w2";
};
nativeBuildInputs = [ cmake ];
buildInputs = [ zlib python2 ];
postFixup = ''
sed -i 's|/usr/bin/env python2|${python2.interpreter}|' $out/lib/python/makeRunScript.py
sed -i 's|/usr/bin/env python|${python2.interpreter}|' $out/lib/python/pyflow/pyflow.py
sed -i 's|/bin/bash|${stdenv.shell}|' $out/lib/python/pyflow/pyflowTaskWrapper.py
'';
doInstallCheck = true;
installCheckPhase = ''
rm $out/lib/python/**/*.pyc
PYTHONPATH=$out/lib/python:$PYTHONPATH python -c 'import makeRunScript'
PYTHONPATH=$out/lib/python/pyflow:$PYTHONPATH python -c 'import pyflowTaskWrapper; import pyflow'
'';
meta = with stdenv.lib; {
description = "Structural variant caller";
license = licenses.gpl3;
homepage = "https://github.com/Illumina/manta";
maintainers = with maintainers; [ jbedo ];
platforms = platforms.x86_64;
};
}

2
pkgs/top-level/all-packages.nix
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@ -23907,6 +23907,8 @@ in
niftyseg = callPackage ../applications/science/biology/niftyseg { };
manta = callPackage ../applications/science/biology/manta { };
octopus-caller = callPackage ../applications/science/biology/octopus { };
paml = callPackage ../applications/science/biology/paml { };