From 851ab7f323c8d369a7cd7d32bdf3d997ebf88518 Mon Sep 17 00:00:00 2001
From: Markus Ankenbrand <markus@ankenbrand.me>
Date: Mon, 25 Jun 2018 16:56:21 +0200
Subject: [PATCH] hmmer: init at 3.1b2

---
 maintainers/maintainer-list.nix               |  5 ++++
 .../science/biology/hmmer/default.nix         | 28 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 ++
 3 files changed, 35 insertions(+)
 create mode 100644 pkgs/applications/science/biology/hmmer/default.nix

diff --git a/maintainers/maintainer-list.nix b/maintainers/maintainer-list.nix
index d99ce88d61ef..4980e44b5b05 100644
--- a/maintainers/maintainer-list.nix
+++ b/maintainers/maintainer-list.nix
@@ -1707,6 +1707,11 @@
     github = "igsha";
     name = "Igor Sharonov";
   };
+  iimog = {
+    email = "iimog@iimog.org";
+    github = "iimog";
+    name = "Markus J. Ankenbrand";
+  };
   ikervagyok = {
     email = "ikervagyok@gmail.com";
     github = "ikervagyok";
diff --git a/pkgs/applications/science/biology/hmmer/default.nix b/pkgs/applications/science/biology/hmmer/default.nix
new file mode 100644
index 000000000000..8552aa34c433
--- /dev/null
+++ b/pkgs/applications/science/biology/hmmer/default.nix
@@ -0,0 +1,28 @@
+{ stdenv, fetchurl }:
+
+stdenv.mkDerivation rec {
+  version = "3.1b2";
+  name = "hmmer-${version}";
+
+  src = fetchurl {
+    url = "http://eddylab.org/software/hmmer3/${version}/${name}.tar.gz";
+    sha256 = "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx";
+  };
+
+  meta = with stdenv.lib; {
+    description = "Biosequence analysis using profile hidden Markov models";
+    longDescription = ''
+HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
+
+HMMER is often used together with a profile database, such as Pfam or many of the databases that participate in Interpro. But HMMER can also work with query sequences, not just profiles, just like BLAST. For example, you can search a protein query sequence against a database with phmmer, or do an iterative search with jackhmmer.
+
+HMMER is designed to detect remote homologs as sensitively as possible, relying on the strength of its underlying probability models. In the past, this strength came at significant computational expense, but as of the new HMMER3 project, HMMER is now essentially as fast as BLAST.
+
+HMMER can be downloaded and installed as a command line tool on your own hardware, and now it is also more widely accessible to the scientific community via new search servers at the European Bioinformatics Institute.
+    '';
+    homepage = http://hmmer.org/;
+    license = licenses.gpl3;
+    maintainers = [ maintainers.iimog ];
+    platforms = platforms.linux;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 0bc2589c7538..8615fa81c718 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -20169,6 +20169,8 @@ with pkgs;
 
   varscan = callPackage ../applications/science/biology/varscan { };
 
+  hmmer = callPackage ../applications/science/biology/hmmer { };
+
   bwa = callPackage ../applications/science/biology/bwa { };
 
   ### SCIENCE/MACHINE LEARNING