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{ lib, fetchFromGitHub, last, exonerate, minia, python3, bwa
, samtools }:
python3.pkgs.buildPythonApplication rec {
pname = "tebreak";
version = "1.1";
src = fetchFromGitHub {
owner = "adamewing";
repo = "tebreak";
rev = version;
sha256 = "13mgh775d8hkl340923lfwwm4r5ps70girn8d6wgfxzwzxylz8iz";
};
nativeBuildInputs = [ python3.pkgs.cython ];
propagatedBuildInputs = with python3.pkgs; [
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
'';
checkPhase = ''
$out/bin/tebreak -b test/data/example.ins.bam -r test/data/Homo_sapiens_chr4_50000000-60000000_assembly19.fasta -p 4 --pickle test/example.pickle --detail_out test/example.tebreak.detail.out -i lib/teref.human.fa
pushd test
${python3.interpreter} checktest.py
'';
meta = with lib; {
description = "Find and characterise transposable element insertions";
mainProgram = "tebreak";
homepage = "https://github.com/adamewing/tebreak";
license = licenses.mit;
maintainers = with maintainers; [ jbedo ];
platforms = platforms.x86_64;
};
}
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