646b892680
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67 lines
1.8 KiB
Nix
67 lines
1.8 KiB
Nix
{
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lib,
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fetchFromGitHub,
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last,
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exonerate,
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minia,
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python3,
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bwa,
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samtools,
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}:
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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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pyproject = true;
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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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build-system = with python3.pkgs; [ setuptools ];
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dependencies = 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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pythonImportsCheck = [ "tebreak" ];
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meta = {
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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 = lib.licenses.mit;
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maintainers = with lib.maintainers; [ jbedo ];
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platforms = lib.platforms.x86_64;
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# Several tests are failing:
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# - AttributeError: module 'skbio.alignment' has no attribute 'local_pairwise_align_ssw'.
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# Did you mean: 'local_pairwise_align'?
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# - AssertionError: 6 != 0
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broken = true;
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};
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}
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