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const std = @import("std");
const builtin = @import("builtin");
const ArrayList = std.ArrayList;
const kalignPackageVersion = "3.5.1";
const targets: []const std.Target.Query = &.{
.{ .cpu_arch = .aarch64, .os_tag = .macos },
.{ .cpu_arch = .aarch64, .os_tag = .linux },
.{ .cpu_arch = .x86_64, .os_tag = .linux, .abi = .gnu },
.{ .cpu_arch = .x86_64, .os_tag = .linux, .abi = .musl },
// .{ .cpu_arch = .x86_64, .os_tag = .windows },
};
const cflags = [_][]const u8{
"-DKALIGN_PACKAGE_VERSION=\"3.5.0\"",
"-DKALIGN_PACKAGE_NAME=\"kalign\"",
"-DKALIGN_ALN_SERIAL_THRESHOLD=250",
"-DKALIGN_KMEANS_UPGMA_THRESHOLD=50",
};
pub fn build(b: *std.Build) !void {
// const target = b.standardTargetOptions(.{});
const optimize = b.standardOptimizeOption(.{});
for (targets) |t| {
const lib = b.addStaticLibrary(.{
.name = "tldevel",
.target = b.resolveTargetQuery(t),
.optimize = optimize,
});
lib.linkLibC();
lib.addIncludePath(.{ .path = "./lib/src" });
lib.addCSourceFiles(.{ .files = &kalign_lib_sources, .flags = &cflags });
lib.addIncludePath(.{ .path = "./lib/include" });
b.installArtifact(lib);
const kalign_bin = b.addExecutable(.{
.name = "kalign",
.target = b.resolveTargetQuery(t),
.optimize = optimize,
});
lib.addCSourceFiles(.{ .files = &kalign_sources, .flags = &cflags });
kalign_bin.addIncludePath(.{ .path = "./lib/src" });
kalign_bin.addIncludePath(.{ .path = "./lib/include" });
kalign_bin.linkLibrary(lib);
b.installArtifact(kalign_bin);
const target_output = b.addInstallArtifact(kalign_bin, .{
.dest_dir = .{
.override = .{
.custom = try t.zigTriple(b.allocator),
},
},
});
b.getInstallStep().dependOn(&target_output.step);
}
// const exe = b.addExecutable(.{
// .name = "zig_test",
// .target = target,
// .optimize = optimize,
// });
// exe.addCSourceFile(.{ .file = .{ .path = "./tests/zig_test.c" }, .flags = &[_][]const u8{"-std=c99"} });
// // exe.addCSourceFiles(.{ .files = &kalign_lib_sources, .flags = &[_][]const u8{"-std=c99"} });
// // exe.addCSourceFile(&.{"./tests/zig_test.c"}, cflags.items);
// // exe.addCSourceFile("./lib/src/strnlen_compat.c", cflags.items);
// exe.addIncludePath(.{ .path = "./lib/src" });
// // exe.linkLibrary(lib);
// exe.linkLibC();
// b.installArtifact(exe);
}
const kalign_lib_sources = [_][]const u8{
// "lib/src/strnlen_compat.c",
"lib/src/test.c",
"lib/src/tldevel.c",
"lib/src/tlmisc.c",
"lib/src/tlrng.c",
"lib/src/esl_stopwatch.c",
"lib/src/msa_alloc.c",
"lib/src/msa_op.c",
"lib/src/msa_io.c",
"lib/src/msa_misc.c",
"lib/src/msa_check.c",
"lib/src/msa_cmp.c",
"lib/src/msa_sort.c",
"lib/src/alphabet.c",
"lib/src/task.c",
"lib/src/bisectingKmeans.c",
"lib/src/sequence_distance.c",
"lib/src/bpm.c",
"lib/src/euclidean_dist.c",
"lib/src/pick_anchor.c",
"lib/src/aln_wrap.c",
"lib/src/aln_apair_dist.c",
"lib/src/aln_param.c",
"lib/src/aln_run.c",
"lib/src/aln_mem.c",
"lib/src/aln_setup.c",
"lib/src/aln_controller.c",
"lib/src/aln_seqseq.c",
"lib/src/aln_seqprofile.c",
"lib/src/aln_profileprofile.c",
"lib/src/aln_refine.c",
"lib/src/sp_score.c",
"lib/src/weave_alignment.c",
"lib/src/poar.c",
"lib/src/consensus_msa.c",
"lib/src/anchor_consistency.c",
"lib/src/ensemble.c",
};
const kalign_sources = [_][]const u8{
"./src/run_kalign.c",
"./src/parameters.c",
};
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