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Use biobricks-ai/dev-shell
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john-shaffer committed Sep 29, 2023
1 parent cc6347b commit 91d0000
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133 changes: 59 additions & 74 deletions flake.lock

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43 changes: 2 additions & 41 deletions flake.nix
Original file line number Diff line number Diff line change
@@ -1,46 +1,7 @@
{
description = "Tox21 biobrick";

inputs = {
nixpkgs.url = "https://flakehub.com/f/NixOS/nixpkgs/*.tar.gz";
flake-utils.url = "https://flakehub.com/f/numtide/flake-utils/*.tar.gz";
biobricks-R = {
url = "github:biobricks-ai/biobricks-R";
inputs.flake-utils.follows = "flake-utils";
inputs.nixpkgs.follows = "nixpkgs";
};
hdt-cpp = {
url = "github:insilica/nix-hdt";
inputs.flake-utils.follows = "flake-utils";
inputs.nixpkgs.follows = "nixpkgs";
};
};
inputs = { dev-shell.url = "github:biobricks-ai/dev-shell"; };

outputs = { self, nixpkgs, flake-utils, biobricks-R, hdt-cpp }:
flake-utils.lib.eachDefaultSystem (system:
with import nixpkgs { inherit system; };
let
# tmducken requires duckdb 0.8.1 or later, and nixos-23.05 only had 0.7
duckdb-version = "0.8.1";
duckdb = (pkgs.duckdb.overrideAttrs (oldAttrs: rec {
version = duckdb-version;
src = fetchFromGitHub {
owner = "duckdb";
repo = "duckdb";
rev = "v${duckdb-version}";
sha256 = "sha256-LEv9yURkYvONObTbIA4CS+umwCRMH8gRQaDtzbCzID4=";
};
}));
in {
devShells.default = mkShell {
buildInputs = [
biobricks-R.packages.${system}.rEnv
clojure
hdt-cpp.packages.${system}.default
duckdb
jdk
];
env = { DUCKDB_HOME = "${duckdb}/lib"; };
};
});
outputs = { self, dev-shell }: { devShells = dev-shell.devShells; };
}

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