ff1a94e523
The nixpkgs-unstable channel's programs.sqlite was used to identify packages producing exactly one binary, and these automatically added to their package definitions wherever possible.
50 lines
1.5 KiB
Nix
50 lines
1.5 KiB
Nix
{ lib, fetchFromGitHub, last, exonerate, minia, python3, bwa
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, samtools }:
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python3.pkgs.buildPythonApplication rec {
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pname = "tebreak";
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version = "1.1";
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src = fetchFromGitHub {
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owner = "adamewing";
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repo = "tebreak";
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rev = version;
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sha256 = "13mgh775d8hkl340923lfwwm4r5ps70girn8d6wgfxzwzxylz8iz";
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};
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nativeBuildInputs = [ python3.pkgs.cython ];
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propagatedBuildInputs = with python3.pkgs; [
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pysam
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scipy
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bx-python
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scikit-bio
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];
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preConfigure = ''
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# patch the paths to all required software
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for f in $(find . -type f) ; do
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sed -i "s|'bwa'|'${bwa}/bin/bwa'|" $f
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sed -i "s|'minia'|'${minia}/bin/minia'|" $f
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sed -i "s|'exonerate'|'${exonerate}/bin/exonerate'|" $f
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sed -i "s|'samtools'|'${samtools}/bin/samtools'|" $f
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sed -i "s|'lastal'|'${last}/bin/lastal'|" $f
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sed -i "s|'lastdb'|'${last}/bin/lastdb'|" $f
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done
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'';
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checkPhase = ''
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$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
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pushd test
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${python3.interpreter} checktest.py
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'';
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meta = with lib; {
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description = "Find and characterise transposable element insertions";
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mainProgram = "tebreak";
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homepage = "https://github.com/adamewing/tebreak";
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license = licenses.mit;
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maintainers = with maintainers; [ jbedo ];
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platforms = platforms.x86_64;
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};
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}
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