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author | Silvan Mosberger <infinisil@icloud.com> | 2018-07-09 04:55:24 +0200 |
---|---|---|
committer | GitHub <noreply@github.com> | 2018-07-09 04:55:24 +0200 |
commit | 8e2c3b93bae2d0bcc020f93ed0dcdb7a206eaf52 (patch) | |
tree | 8b23dfd3b50ef6b5cab9b973f5ec9aacaf1f425b /pkgs | |
parent | 1dd7bc7dfcd3e6d3529f5436b3d5aecf6c3fe74c (diff) | |
parent | 59141de608a0723179b5164ff59d42b69782b3fa (diff) |
Merge pull request #43096 from jbedo/mosdepth
mosdepth: init 0.2.3
Diffstat (limited to 'pkgs')
-rw-r--r-- | pkgs/applications/science/biology/mosdepth/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/mosdepth/default.nix b/pkgs/applications/science/biology/mosdepth/default.nix new file mode 100644 index 0000000000000..05cd7992aa900 --- /dev/null +++ b/pkgs/applications/science/biology/mosdepth/default.nix @@ -0,0 +1,42 @@ +{stdenv, fetchFromGitHub, nim, htslib, patchelf, pcre}: + +let + hts-nim = fetchFromGitHub { + owner = "brentp"; + repo = "hts-nim"; + rev = "9cd83e30522ab64cd71eb8209be4154aa5579ce1"; + sha256 = "10g408idy14667varq1syf06rrbpk63i3ib7i5dh1md4ib19av6f"; + }; + + docopt = fetchFromGitHub { + owner = "docopt"; + repo = "docopt.nim"; + rev = "v0.6.5"; + sha256 = "0yx79m4jkdcazwlky55nwf39zj5kdhymrrdrjq29mahiwx83x5zr"; + }; + +in stdenv.mkDerivation rec { + name = "mosdepth-${version}"; + version = "0.2.3"; + + src = fetchFromGitHub { + owner = "brentp"; + repo = "mosdepth"; + rev = "v${version}"; + sha256 = "1b9frrwhcvay3alhn0d02jccc2qlbij1732hzq9nhwnr4kvsvxx7"; + }; + + buildInputs = [ nim ]; + + buildPhase = "nim -p:${hts-nim}/src -p:${docopt}/src c -d:release mosdepth.nim"; + installPhase = "install -Dt $out/bin mosdepth"; + fixupPhase = "patchelf --set-rpath ${stdenv.lib.makeLibraryPath [ stdenv.cc.cc htslib pcre ]} $out/bin/mosdepth"; + + meta = with stdenv.lib; { + description = "fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing."; + license = licenses.mit; + homepage = https://github.com/brentp/mosdepth; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.linux; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 2e8285db1aab4..d601776c6bfd1 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -20264,6 +20264,8 @@ with pkgs; minimap2 = callPackage ../applications/science/biology/minimap2 { }; + mosdepth = callPackage ../applications/science/biology/mosdepth { }; + ncbi_tools = callPackage ../applications/science/biology/ncbi-tools { }; paml = callPackage ../applications/science/biology/paml { }; |