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author | Justin Bedo <cu@cua0.org> | 2021-01-05 10:18:55 +1100 |
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committer | tomberek <tomberek@users.noreply.github.com> | 2021-03-28 22:27:51 -0400 |
commit | 76bd95316205e1eaf472b04fceef654f0e7639a1 (patch) | |
tree | c3b7c6d60bf21f19cff626799808c089ceed8568 /pkgs/applications/science | |
parent | 632ae0892e884a0777fafb364d8ec7728aaee487 (diff) | |
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bedops: init 2.4.39
Diffstat (limited to 'pkgs/applications/science')
-rw-r--r-- | pkgs/applications/science/biology/bedops/default.nix | 51 |
1 files changed, 51 insertions, 0 deletions
diff --git a/pkgs/applications/science/biology/bedops/default.nix b/pkgs/applications/science/biology/bedops/default.nix new file mode 100644 index 00000000000..407ed0c01f7 --- /dev/null +++ b/pkgs/applications/science/biology/bedops/default.nix @@ -0,0 +1,51 @@ +{ lib, stdenv, fetchFromGitHub, zlib, bzip2, jansson, makeWrapper }: + +stdenv.mkDerivation rec { + pname = "bedops"; + version = "2.4.39"; + + src = fetchFromGitHub { + owner = "bedops"; + repo = "bedops"; + rev = "v${version}"; + sha256 = "sha256-vPrut3uhZK1Eg9vPcyxVNWW4zKeypdsb28oM1xbbpJo="; + }; + + buildInputs = [ zlib bzip2 jansson ]; + nativeBuildInputs = [ makeWrapper ]; + + preConfigure = '' + # We use nixpkgs versions of these libraries + rm -r third-party + sed -i '/^LIBS/d' system.mk/* + sed -i 's|^LIBRARIES.*$|LIBRARIES = -lbz2 -lz -ljansson|' */*/*/*/Makefile + substituteInPlace applications/bed/starch/src/Makefile --replace '$(LIBRARIES)' "" + + # Function name is different in nixpkgs provided libraries + for f in interfaces/src/data/starch/starchFileHelpers.c applications/bed/starch/src/starchcat.c ; do + substituteInPlace $f --replace deflateInit2cpp deflateInit2 + done + + # Don't force static + for f in */*/*/*/Makefile ; do + substituteInPlace $f --replace '-static' "" + done + ''; + + makeFlags = [ "BINDIR=$(out)/bin" ]; + + postFixup = '' + for f in $out/bin/* ; do + wrapProgram $f --prefix PATH : "$out/bin" + done + ''; + + meta = with lib; { + description = "Suite of tools for addressing questions arising in genomics studies"; + homepage = "https://github.com/bedops/bedops"; + license = licenses.gpl2Only; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.x86_64; + broken = stdenv.isDarwin; + }; +} |