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571c71e6f7
We are migrating packages that meet below requirements:
1. using `callPackage`
2. called path is a directory
3. overriding set is empty (`{ }`)
4. not containing path expressions other than relative path (to
makenixpkgs-vet happy)
5. not referenced by nix files outside of the directory, other
than`pkgs/top-level/all-packages.nix`
6. not referencing nix files outside of the directory
7. not referencing `default.nix` (since it's changed to `package.nix`)
8. `outPath` doesn't change after migration
The tool is here: https://github.com/Aleksanaa/by-name-migrate.
64 lines
1.9 KiB
Nix
64 lines
1.9 KiB
Nix
{ lib, stdenv, fetchFromGitHub, zlib, bzip2, jansson, makeWrapper }:
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stdenv.mkDerivation rec {
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pname = "bedops";
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version = "2.4.41";
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src = fetchFromGitHub {
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owner = "bedops";
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repo = "bedops";
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rev = "v${version}";
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sha256 = "sha256-VJBoi1+tHA4oOVOsClUfimB+mOV5ZSQsDcDq3vAZwBA=";
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};
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buildInputs = [ zlib bzip2 jansson ];
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nativeBuildInputs = [ makeWrapper ];
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preConfigure = ''
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# We use nixpkgs versions of these libraries
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rm -r third-party
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sed -i '/^LIBS/d' system.mk/*
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sed -i 's|^LIBRARIES.*$|LIBRARIES = -lbz2 -lz -ljansson|' */*/*/*/Makefile*
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# `make support` installs above libraries
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substituteInPlace system.mk/* \
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--replace ": support" ":"
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# Variable name is different in this makefile
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substituteInPlace applications/bed/sort-bed/src/Makefile.darwin \
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--replace "DIST_DIR" "BINDIR"
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# `mkdir -p $BINDIR` is missing
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substituteInPlace applications/bed/sort-bed/src/Makefile.darwin \
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--replace 'mkdir -p ''${OBJ_DIR}' 'mkdir -p ''${OBJ_DIR} ''${BINDIR}'
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substituteInPlace applications/bed/starch/src/Makefile --replace '$(LIBRARIES)' ""
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# Function name is different in nixpkgs provided libraries
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for f in interfaces/src/data/starch/starchFileHelpers.c applications/bed/starch/src/starchcat.c ; do
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substituteInPlace $f --replace deflateInit2cpp deflateInit2
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done
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# Don't force static
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for f in */*/*/*/Makefile* ; do
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substituteInPlace $f --replace '-static' ""
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done
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'';
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makeFlags = [ "BINDIR=$(out)/bin" ];
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postFixup = ''
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for f in $out/bin/* ; do
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wrapProgram $f --prefix PATH : "$out/bin"
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done
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'';
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meta = with lib; {
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description = "Suite of tools for addressing questions arising in genomics studies";
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homepage = "https://github.com/bedops/bedops";
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license = licenses.gpl2Only;
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maintainers = with maintainers; [ jbedo ];
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platforms = platforms.x86_64;
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};
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}
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