43 lines
1.2 KiB
Nix
43 lines
1.2 KiB
Nix
|
{ 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;
|
||
|
|
};
|
||
|
|
}
|