From 13a1f2c296efd872a4ff9720be34e1a28700a075 Mon Sep 17 00:00:00 2001
From: Luis Pedro Coelho <luis@luispedro.org>
Date: Mon, 15 Apr 2019 08:22:47 +0800
Subject: [PATCH] eggnog-mapper: init at 1.0.3 (#58905)

---
 .../science/biology/eggnog-mapper/default.nix | 40 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 +
 2 files changed, 42 insertions(+)
 create mode 100644 pkgs/applications/science/biology/eggnog-mapper/default.nix

diff --git a/pkgs/applications/science/biology/eggnog-mapper/default.nix b/pkgs/applications/science/biology/eggnog-mapper/default.nix
new file mode 100644
index 00000000000..a15425ec213
--- /dev/null
+++ b/pkgs/applications/science/biology/eggnog-mapper/default.nix
@@ -0,0 +1,40 @@
+{ stdenv, fetchFromGitHub, fetchpatch, makeWrapper, python27Packages, wget, diamond, hmmer }:
+
+python27Packages.buildPythonApplication rec {
+  pname = "eggnog-mapper";
+  version = "1.0.3";
+
+  src = fetchFromGitHub {
+    owner = "eggnogdb";
+    repo = "eggnog-mapper";
+    rev = "${version}";
+    sha256 = "1aaaflppy84bhkh2hb5gnzm4xgrz0rz0cgfpadr9w8cva8p0sqdv";
+  };
+
+  patches = (fetchpatch {
+    url = https://github.com/eggnogdb/eggnog-mapper/pull/125/commits/b7828e4c8c1c453e391aef050f06ff3f84ff9faf.patch;
+    sha256 = "0nz1a7ybm4j5c7vdm3annnxz9036iam2044hia341a0am9wydmzk";
+  });
+
+  buildInputs = [ makeWrapper ];
+  propagatedBuildInputs = [ python27Packages.biopython wget diamond hmmer ];
+
+  # make emapper find diamond & hmmer
+  makeWrapperArgs = [
+    ''--prefix PATH ':' "${diamond}/bin"''
+    ''--prefix PATH ':' "${hmmer}/bin"''
+    ];
+
+  # Tests rely on some of the databases being available, which is not bundled
+  # with this package as (1) in total, they represent >100GB of data, and (2)
+  # the user can download only those that interest them.
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "Fast genome-wide functional annotation through orthology assignment";
+    license = licenses.gpl2;
+    homepage = https://github.com/eggnogdb/eggnog-mapper/wiki;
+    maintainers = with maintainers; [ luispedro ];
+    platforms = platforms.all;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 3a37d96330a..13e7382f6cd 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -21828,6 +21828,8 @@ in
 
   ecopcr = callPackage ../applications/science/biology/ecopcr { };
 
+  eggnog-mapper = callPackage ../applications/science/biology/eggnog-mapper { };
+
   emboss = callPackage ../applications/science/biology/emboss { };
 
   ezminc = callPackage ../applications/science/biology/EZminc { };