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author | Martin Weinelt <hexa@darmstadt.ccc.de> | 2022-01-12 02:33:33 +0100 |
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committer | Martin Weinelt <hexa@darmstadt.ccc.de> | 2022-01-16 02:36:23 +0100 |
commit | 492e5e07c9f2d622e776fcc2887ecded5edf0a43 (patch) | |
tree | 553c7657da77944963235e43744e98ca8a8ca2ec /pkgs/applications/science | |
parent | 369db3b2f321c8fe263084dd876dfb3a330b36cf (diff) | |
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lumpy: drop
Removed because it requires python2 and the upstream repository looks undermaintained.
Diffstat (limited to 'pkgs/applications/science')
-rw-r--r-- | pkgs/applications/science/biology/lumpy/default.nix | 50 |
1 files changed, 0 insertions, 50 deletions
diff --git a/pkgs/applications/science/biology/lumpy/default.nix b/pkgs/applications/science/biology/lumpy/default.nix deleted file mode 100644 index 91a00174447..00000000000 --- a/pkgs/applications/science/biology/lumpy/default.nix +++ /dev/null @@ -1,50 +0,0 @@ -{ lib, stdenv, fetchFromGitHub, htslib, zlib, curl, openssl, samblaster, sambamba -, samtools, hexdump, python2Packages, which }: - -let - python = - python2Packages.python.withPackages (pkgs: with pkgs; [ pysam numpy ]); - -in stdenv.mkDerivation rec { - pname = "lumpy"; - version = "0.3.1"; - - src = fetchFromGitHub { - owner = "arq5x"; - repo = "lumpy-sv"; - rev = "v${version}"; - sha256 = "0r71sg7qch8r6p6dw995znrqdj6q49hjdylhzbib2qmv8nvglhs9"; - fetchSubmodules = true; - }; - - nativeBuildInputs = [ which ]; - buildInputs = - [ htslib zlib curl openssl python samblaster sambamba samtools hexdump ]; - - preConfigure = '' - patchShebangs ./. - - # Use Nix htslib over bundled version - sed -i 's/lumpy_filter: htslib/lumpy_filter:/' Makefile - sed -i 's|../../lib/htslib/libhts.a|-lhts|' src/filter/Makefile - # Also make sure we use the includes from Nix's htslib - sed -i 's|../../lib/htslib/|${htslib}|' src/filter/Makefile - ''; - - # Upstream's makefile doesn't have an install target - installPhase = '' - mkdir -p $out - cp -r bin $out - cp -r scripts $out - sed -i 's|/build/source|'$out'|' $out/bin/lumpyexpress.config - ''; - - meta = with lib; { - description = "Probabilistic structural variant caller"; - homepage = "https://github.com/arq5x/lumpy-sv"; - maintainers = with maintainers; [ jbedo ]; - license = licenses.mit; - platforms = [ "x86_64-linux" ]; - }; - -} |