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{ stdenv, fetchFromGitHub, last, exonerate, minia, python3Packages, bwa
, samtools, findutils }:
python3Packages.buildPythonApplication rec {
pname = "tebreak";
version = "1.0";
src = fetchFromGitHub {
owner = "adamewing";
repo = "tebreak";
rev = version;
sha256 = "194av17wz66n4zxyi56mbkik31j2wmkly5i9qmxgaxymhavzi3kq";
};
nativeBuildInputs = [ findutils python3Packages.cython ];
propagatedBuildInputs = with python3Packages; [
pysam
scipy
bx-python
scikit-bio
];
preConfigure = ''
# patch the paths to all required software
for f in $(find . -type f) ; do
sed -i "s|'bwa'|'${bwa}/bin/bwa'|" $f
sed -i "s|'minia'|'${minia}/bin/minia'|" $f
sed -i "s|'exonerate'|'${exonerate}/bin/exonerate'|" $f
sed -i "s|'samtools'|'${samtools}/bin/samtools'|" $f
sed -i "s|'lastal'|'${last}/bin/lastal'|" $f
sed -i "s|'lastdb'|'${last}/bin/lastdb'|" $f
done
'';
meta = with stdenv.lib; {
description = "Find and characterise transposable element insertions";
homepage = "https://github.com/adamewing/tebreak";
license = licenses.mit;
maintainers = with maintainers; [ jbedo ];
platforms = platforms.x86_64;
};
}
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