diff options
Diffstat (limited to 'pkgs/applications')
-rw-r--r-- | pkgs/applications/science/biology/tebreak/default.nix | 42 |
1 files changed, 42 insertions, 0 deletions
diff --git a/pkgs/applications/science/biology/tebreak/default.nix b/pkgs/applications/science/biology/tebreak/default.nix new file mode 100644 index 00000000000..9ff81944f6a --- /dev/null +++ b/pkgs/applications/science/biology/tebreak/default.nix @@ -0,0 +1,42 @@ +{ 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; + }; +} |