587713944a
GitOrigin-RevId: 6143fc5eeb9c4f00163267708e26191d1e918932
49 lines
1.5 KiB
Nix
49 lines
1.5 KiB
Nix
{ 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;
|
|
};
|
|
}
|