diff options
| author | Justin Bedo <cu@cua0.org> | 2019-12-18 17:36:31 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-12-29 17:16:10 +1100 |
| commit | 11460d4cac3a7cd744522511f2f6cf68cbfff8ff (patch) | |
| tree | 876495173d5ebf30a152e1098123f7d28063209c | |
| parent | 21919122744688bb919ad1fa6b84cf8ee100b1e7 (diff) | |
| download | nixlib-11460d4cac3a7cd744522511f2f6cf68cbfff8ff.tar nixlib-11460d4cac3a7cd744522511f2f6cf68cbfff8ff.tar.gz nixlib-11460d4cac3a7cd744522511f2f6cf68cbfff8ff.tar.bz2 nixlib-11460d4cac3a7cd744522511f2f6cf68cbfff8ff.tar.lz nixlib-11460d4cac3a7cd744522511f2f6cf68cbfff8ff.tar.xz nixlib-11460d4cac3a7cd744522511f2f6cf68cbfff8ff.tar.zst nixlib-11460d4cac3a7cd744522511f2f6cf68cbfff8ff.zip | |
tebreak: init at 1.0
| -rw-r--r-- | pkgs/applications/science/biology/tebreak/default.nix | 42 | ||||
| -rw-r--r-- | pkgs/top-level/all-packages.nix | 2 |
2 files changed, 44 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 000000000000..9ff81944f6a7 --- /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; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index be2ae96387a9..73e5304749e3 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -23677,6 +23677,8 @@ in svaba = callPackage ../applications/science/biology/svaba { }; + tebreak = callPackage ../applications/science/biology/tebreak { }; + trimal = callPackage ../applications/science/biology/trimal { }; truvari = callPackage ../applications/science/biology/truvari { }; |