From 0bbaae30381cf7a83f9d9ddc9f3b573aa81beb4f Mon Sep 17 00:00:00 2001
From: Tyson Whitehead <twhitehead@gmail.com>
Date: Thu, 7 Nov 2019 17:27:33 -0500
Subject: [PATCH] smoove: Initial packaging

---
 pkgs/all-packages.nix   |   2 +
 pkgs/smoove/default.nix |  41 +++++++
 pkgs/smoove/deps.nix    | 237 ++++++++++++++++++++++++++++++++++++++++
 3 files changed, 280 insertions(+)
 create mode 100644 pkgs/smoove/default.nix
 create mode 100644 pkgs/smoove/deps.nix

diff --git a/pkgs/all-packages.nix b/pkgs/all-packages.nix
index 013d09f..a401ff3 100644
--- a/pkgs/all-packages.nix
+++ b/pkgs/all-packages.nix
@@ -48,6 +48,8 @@ self: super: pkgs: with pkgs; {
 
   rOverrides = lib.composeExtensions super.rOverrides (import ./r-modules.nix pkgs);
 
+  smoove = callPackage ./smoove { };
+
   #sumo = callPackage ./sumo.nix { fox = fox_1_6; };
 
   namd = callPackage ./namd.nix { };
diff --git a/pkgs/smoove/default.nix b/pkgs/smoove/default.nix
new file mode 100644
index 0000000..ebd7c56
--- /dev/null
+++ b/pkgs/smoove/default.nix
@@ -0,0 +1,41 @@
+# This file was generated by https://github.com/kamilchm/go2nix v1.3.0
+{ stdenv, buildGoPackage, fetchgit, fetchhg, fetchbzr, fetchsvn, makeWrapper
+, gzip, gsort, htslib, lumpy, samtools, svtyper, mosdepth }:
+
+buildGoPackage rec {
+  name = "smoove-${version}";
+  version = "0.2.4";
+
+  goPackagePath = "github.com/brentp/smoove";
+
+  src = fetchgit {
+    rev = "v${version}";
+    url = "https://github.com/brentp/smoove.git";
+    sha256 = "0jyycc3rjy406qkc17pfagy44bnkmgk348plqwqqpcawdpwpj57v";
+  };
+
+  postFixup = ''
+    declare -p
+    wrapProgram "$bin/bin/smoove"        \
+      --suffix PATH : "${gzip}/bin"      \
+      --suffix PATH : "${gsort}/bin"     \
+      --suffix PATH : "${htslib}/bin"    \
+      --suffix PATH : "${lumpy}/bin"     \
+      --suffix PATH : "${samtools}/bin"  \
+      --suffix PATH : "${svtyper}/bin"   \
+      --suffix PATH : "${mosdepth}/bin"
+  '';
+
+  goDeps = ./deps.nix;
+
+  nativeBuildInputs = [
+    makeWrapper
+  ];
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/brentp/smoove;
+    description = "Wrap existing software and adds some internal read-filtering to simplify calling and genotyping structural variants.";
+    platforms = platforms.all;
+    license = licenses.asl20;
+  };
+}
diff --git a/pkgs/smoove/deps.nix b/pkgs/smoove/deps.nix
new file mode 100644
index 0000000..4303037
--- /dev/null
+++ b/pkgs/smoove/deps.nix
@@ -0,0 +1,237 @@
+# This file was generated by https://github.com/kamilchm/go2nix v1.3.0
+[
+  {
+    goPackagePath = "github.com/ajstarks/svgo";
+    fetch = {
+      type = "git";
+      url = "https://github.com/ajstarks/svgo";
+      rev = "de52242f3d65700ff4fa20a246fd17c8fcfc1d09";
+      sha256 = "16wns7ny1r836gyf41hdrg2fwa61bb4mffq86511fyqbyyghi9rd";
+    };
+  }
+  {
+    goPackagePath = "github.com/alexflint/go-arg";
+    fetch = {
+      type = "git";
+      url = "https://github.com/alexflint/go-arg";
+      rev = "c0c7a3ba8a1854cd85e65cca4f0e2028698a0738";
+      sha256 = "19vcwh799521rvs4cyplkmw5jw07xqrmvxicf1x57mqgg4y4rapx";
+    };
+  }
+  {
+    goPackagePath = "github.com/biogo/biogo";
+    fetch = {
+      type = "git";
+      url = "https://github.com/biogo/biogo";
+      rev = "44dd7037cce173b0211112bb93b8303e689a06f4";
+      sha256 = "0hsbd83y0wlzc1w3man9469wqz1csf19gxz8fzrpb35gdiby5bc0";
+    };
+  }
+  {
+    goPackagePath = "github.com/biogo/hts";
+    fetch = {
+      type = "git";
+      url = "https://github.com/biogo/hts";
+      rev = "a62306de25dd5e4098a34b327ad616a59d245c02";
+      sha256 = "1cx024gdnydhr17bn87ymayqfpxa4p9slpqn5yjjq6br5n9bb3ab";
+    };
+  }
+  {
+    goPackagePath = "github.com/biogo/store";
+    fetch = {
+      type = "git";
+      url = "https://github.com/biogo/store";
+      rev = "884f370e325d9036057c7cf5167ca8a05fba575a";
+      sha256 = "1wzqva9npcgxlsahxj1309wshfp17mfnbzvmzfap7sbvzi99xpwh";
+    };
+  }
+  {
+    goPackagePath = "github.com/brentp/faidx";
+    fetch = {
+      type = "git";
+      url = "https://github.com/brentp/faidx";
+      rev = "d1dc6b6bb739d1f6dbfce95769b351e3449b12a9";
+      sha256 = "0w7nss2l0kiai1ddcgavfjcqrnfqqcb2ic8hh9dwwz2521kbv5qm";
+    };
+  }
+  {
+    goPackagePath = "github.com/brentp/gargs";
+    fetch = {
+      type = "git";
+      url = "https://github.com/brentp/gargs";
+      rev = "92b4f780cf60cfcd09f472605d7325c9092b2561";
+      sha256 = "0698rxcx0cq9c42bljshljyy2xv9wgc26niwpm17ckycr6m2pzzy";
+    };
+  }
+  {
+    goPackagePath = "github.com/brentp/go-athenaeum";
+    fetch = {
+      type = "git";
+      url = "https://github.com/brentp/go-athenaeum";
+      rev = "19f838fd53ded7597276a21998f976dcc5b47dc5";
+      sha256 = "01p6s98b0vrylzgfjbqmjryx92v5qyw8f8n704r7nvh4la44q943";
+    };
+  }
+  {
+    goPackagePath = "github.com/brentp/go-chartjs";
+    fetch = {
+      type = "git";
+      url = "https://github.com/brentp/go-chartjs";
+      rev = "a37b166b7875a9d98fbc944508deaa0fb7c7f128";
+      sha256 = "1r5dhsdqhx1zxr1zic2y4kmhnq25l9i6iszbsfjsppwp9hyvknqx";
+    };
+  }
+  {
+    goPackagePath = "github.com/brentp/goleft";
+    fetch = {
+      type = "git";
+      url = "https://github.com/brentp/goleft";
+      rev = "1ab7eb6d1a1f57de0e5f2764aa1a2ad8ee2d7390";
+      sha256 = "1mn1a20yylr6w5q25fl5yz6dvxqvq4lqk8r2yyy37dsxd9laly9j";
+    };
+  }
+  {
+    goPackagePath = "github.com/brentp/irelate";
+    fetch = {
+      type = "git";
+      url = "https://github.com/brentp/irelate";
+      rev = "1bf7c8f95c75ca1dc016bf9b71d26f12d6da6338";
+      sha256 = "1jmj0f4hldwcmmr64r833lks2fp063dg7azpblc7yy80w20v2n11";
+    };
+  }
+  {
+    goPackagePath = "github.com/brentp/vcfgo";
+    fetch = {
+      type = "git";
+      url = "https://github.com/brentp/vcfgo";
+      rev = "654ed2e5945df15eabbc671fb16556289533f136";
+      sha256 = "1aa7129xagp3hy8waj4x9n9h4yrwwh3hx53xfxrp17db211lnjz4";
+    };
+  }
+  {
+    goPackagePath = "github.com/brentp/xopen";
+    fetch = {
+      type = "git";
+      url = "https://github.com/brentp/xopen";
+      rev = "111b45cadc7d8be411420143ce0873a889c90227";
+      sha256 = "027nzdcxm1nylj1h25085k1xyz430m7g2qb3ni7j45jviypsffxw";
+    };
+  }
+  {
+    goPackagePath = "github.com/edsrzf/mmap-go";
+    fetch = {
+      type = "git";
+      url = "https://github.com/edsrzf/mmap-go";
+      rev = "904c4ced31cdffe19e971afa0b3d319ff06d9c72";
+      sha256 = "0vxww5l4wc449f6r1hwyg8k88bf5i8q8s6sjq9jd24yqpva35c84";
+    };
+  }
+  {
+    goPackagePath = "github.com/fatih/color";
+    fetch = {
+      type = "git";
+      url = "https://github.com/fatih/color";
+      rev = "3f9d52f7176a6927daacff70a3e8d1dc2025c53e";
+      sha256 = "165ww24x6ba47ji4j14mp3f006ksnmi53ws9280pgd2zcw91nbn8";
+    };
+  }
+  {
+    goPackagePath = "github.com/fogleman/gg";
+    fetch = {
+      type = "git";
+      url = "https://github.com/fogleman/gg";
+      rev = "4dc34561c649343936bb2d29e23959bd6d98ab12";
+      sha256 = "1x1finzdrr80dd3r7wvf7zb184yjf4dawz7s581p2dr64dcialww";
+    };
+  }
+  {
+    goPackagePath = "github.com/golang/freetype";
+    fetch = {
+      type = "git";
+      url = "https://github.com/golang/freetype";
+      rev = "e2365dfdc4a05e4b8299a783240d4a7d5a65d4e4";
+      sha256 = "194w3djc6fv1rgcjqds085b9fq074panc5vw582bcb8dbfzsrqxc";
+    };
+  }
+  {
+    goPackagePath = "github.com/jung-kurt/gofpdf";
+    fetch = {
+      type = "git";
+      url = "https://github.com/jung-kurt/gofpdf";
+      rev = "24bd947b7f36dba098261ed6773c281383b04609";
+      sha256 = "1hbcvjqcb2i7bazvia8nch2d426g7y2cr9ibvwzr7dfx4619pnvp";
+    };
+  }
+  {
+    goPackagePath = "github.com/mattn/go-isatty";
+    fetch = {
+      type = "git";
+      url = "https://github.com/mattn/go-isatty";
+      rev = "0e9ddb7c0c0aef74fa25eaba4141e6b5ab7aca2a";
+      sha256 = "0rb5dsp54kg9vjz4qa7b352idvs6pcmchn5xqa4n4kmjhfq5vcjv";
+    };
+  }
+  {
+    goPackagePath = "github.com/pkg/errors";
+    fetch = {
+      type = "git";
+      url = "https://github.com/pkg/errors";
+      rev = "27936f6d90f9c8e1145f11ed52ffffbfdb9e0af7";
+      sha256 = "0yzmgi6g4ak4q8y7w6x0n5cbinlcn8yc3gwgzy4yck00qdn25d6y";
+    };
+  }
+  {
+    goPackagePath = "github.com/valyala/bytebufferpool";
+    fetch = {
+      type = "git";
+      url = "https://github.com/valyala/bytebufferpool";
+      rev = "cdfbe9377474227bb42120c1e22fd4433e7f69bf";
+      sha256 = "0c6cixd85dvl2gvs7sdh0k2wm8r3grl4fw0jg4w7d78cp8s2k7ag";
+    };
+  }
+  {
+    goPackagePath = "github.com/valyala/fasttemplate";
+    fetch = {
+      type = "git";
+      url = "https://github.com/valyala/fasttemplate";
+      rev = "8fcc7a99b5795b7c3e95172237cf93282fc339a9";
+      sha256 = "089wm839lqmw9knr3ifbi82iykaybk0zxzp3c02lsh31wax4f8a2";
+    };
+  }
+  {
+    goPackagePath = "golang.org/x/image";
+    fetch = {
+      type = "git";
+      url = "https://go.googlesource.com/image";
+      rev = "e7c1f5e7dbb87d8921928a6d9fc52fb31ce73b24";
+      sha256 = "0czp897aicqw1dgybj0hc2zzwb20rhqkdqm7siqci3yk7yk9cymf";
+    };
+  }
+  {
+    goPackagePath = "golang.org/x/sys";
+    fetch = {
+      type = "git";
+      url = "https://go.googlesource.com/sys";
+      rev = "ac3223d8017937d8cd94de35a801ea2459f6d5a0";
+      sha256 = "1vgbbsf1b0aazzjnxrlfl6y54cvlkiy76d7rpgl8b6wvc6kzfnk2";
+    };
+  }
+  {
+    goPackagePath = "gonum.org/v1/gonum";
+    fetch = {
+      type = "git";
+      url = "https://github.com/gonum/gonum";
+      rev = "586a766cd0517641931edf76433230b6ece698a0";
+      sha256 = "0yn9achcwc8zykkfi4n7zyvqzg78dh1pzd7890faxi41541ib3cw";
+    };
+  }
+  {
+    goPackagePath = "gonum.org/v1/plot";
+    fetch = {
+      type = "git";
+      url = "https://github.com/gonum/plot";
+      rev = "159cd04f920ca18b61d1519750de83b685c7bddc";
+      sha256 = "0gsms9w71smdd3l2zd4h599fdn9yizychf5gc4j1616ffsm4prq0";
+    };
+  }
+]