From e68e028a52590fc4dd35aca568c015208829a88e Mon Sep 17 00:00:00 2001
From: FX Coudert <fxcoudert@gmail.com>
Date: Sat, 13 Jan 2018 15:08:16 +0100
Subject: [PATCH 1/4] konoha: phase out :mpi

---
 Formula/konoha.rb | 17 +++++------------
 1 file changed, 5 insertions(+), 12 deletions(-)

diff --git a/Formula/konoha.rb b/Formula/konoha.rb
index 8c0f01d6764e3..276e8fb0c3674 100644
--- a/Formula/konoha.rb
+++ b/Formula/konoha.rb
@@ -3,7 +3,7 @@ class Konoha < Formula
   homepage "https://github.com/konoha-project/konoha3"
   url "https://github.com/konoha-project/konoha3/archive/v0.1.tar.gz"
   sha256 "e7d222808029515fe229b0ce1c4e84d0a35b59fce8603124a8df1aeba06114d3"
-  revision 2
+  revision 3
 
   bottle do
     sha256 "02bc662f7d21b3a4a0de5fe3ab0687ad686ca7dc67fe22374abd75a34a33f78b" => :high_sierra
@@ -17,25 +17,18 @@ class Konoha < Formula
     depends_on "openssl"
   end
 
-  option "with-test", "Verify the build with make test (May currently fail)"
-
-  deprecated_option "tests" => "with-test"
-
   depends_on "cmake" => :build
-  depends_on :mpi => [:cc, :cxx]
-  depends_on "pcre"
   depends_on "json-c"
-  depends_on "sqlite"
   depends_on "mecab" if MacOS.version >= :mountain_lion
-  depends_on "python" if MacOS.version <= :snow_leopard # for python glue code
+  depends_on "open-mpi"
+  depends_on "pcre"
+  depends_on "python" if MacOS.version <= :snow_leopard
+  depends_on "sqlite"
 
   def install
     mkdir "build" do
       system "cmake", "..", *std_cmake_args
       system "make"
-      # `make test` currently fails. Reported upstream:
-      # https://github.com/konoha-project/konoha3/issues/438
-      system "make", "test" if build.with? "test"
       system "make", "install"
     end
   end

From 49ab21c12a3915cc4d15b86422efe5f881184b47 Mon Sep 17 00:00:00 2001
From: FX Coudert <fxcoudert@gmail.com>
Date: Sat, 13 Jan 2018 15:08:51 +0100
Subject: [PATCH 2/4] abyss: phase out :mpi

---
 Formula/abyss.rb | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/Formula/abyss.rb b/Formula/abyss.rb
index 92c55ff011b7a..fa300358a2363 100644
--- a/Formula/abyss.rb
+++ b/Formula/abyss.rb
@@ -3,7 +3,7 @@ class Abyss < Formula
   homepage "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
   url "https://github.com/bcgsc/abyss/releases/download/2.0.2/abyss-2.0.2.tar.gz"
   sha256 "d87b76edeac3a6fb48f24a1d63f243d8278a324c9a5eb29027b640f7089422df"
-  revision 2
+  revision 3
 
   bottle do
     cellar :any
@@ -20,12 +20,12 @@ class Abyss < Formula
     depends_on "multimarkdown" => :build
   end
 
-  needs :openmp
-
   depends_on "boost" => :build
   depends_on "google-sparsehash" => :build
   depends_on "gcc"
-  depends_on :mpi => :cc
+  depends_on "open-mpi"
+
+  fails_with :clang # no OpenMP support
 
   resource("testdata") do
     url "http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.3.4/test-data.tar.gz"

From 09f0060965a20619f80cf8a57e5fdc8b02c75f96 Mon Sep 17 00:00:00 2001
From: FX Coudert <fxcoudert@gmail.com>
Date: Sat, 13 Jan 2018 15:09:37 +0100
Subject: [PATCH 3/4] bsponmpi: phase out :mpi

---
 Formula/bsponmpi.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Formula/bsponmpi.rb b/Formula/bsponmpi.rb
index 85d3817534097..1e529dc1f1198 100644
--- a/Formula/bsponmpi.rb
+++ b/Formula/bsponmpi.rb
@@ -3,7 +3,7 @@ class Bsponmpi < Formula
   homepage "https://sourceforge.net/projects/bsponmpi/"
   url "https://downloads.sourceforge.net/project/bsponmpi/bsponmpi/0.3/bsponmpi-0.3.tar.gz"
   sha256 "bc90ca22155be9ff65aca4e964d8cd0bef5f0facef0a42bc1db8b9f822c92a90"
-  revision 1
+  revision 2
 
   bottle do
     sha256 "2d3c362d85b10c9a1bd1b4adc45ac2576abe0a86c15408d20c375bffd9e05494" => :high_sierra
@@ -12,7 +12,7 @@ class Bsponmpi < Formula
   end
 
   depends_on "scons" => :build
-  depends_on :mpi => [:cc, :cxx]
+  depends_on "open-mpi"
 
   def install
     # Don't install 'CVS' folders from tarball

From 7cb3bba5a9506181c5687363d97d0afc1f72a1d8 Mon Sep 17 00:00:00 2001
From: FX Coudert <fxcoudert@gmail.com>
Date: Sat, 13 Jan 2018 15:11:39 +0100
Subject: [PATCH 4/4] boost-mpi: phase out :mpi

---
 Formula/boost-mpi.rb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Formula/boost-mpi.rb b/Formula/boost-mpi.rb
index 819937c86b032..83c549992360d 100644
--- a/Formula/boost-mpi.rb
+++ b/Formula/boost-mpi.rb
@@ -3,6 +3,7 @@ class BoostMpi < Formula
   homepage "https://www.boost.org/"
   url "https://dl.bintray.com/boostorg/release/1.66.0/source/boost_1_66_0.tar.bz2"
   sha256 "5721818253e6a0989583192f96782c4a98eb6204965316df9f5ad75819225ca9"
+  revision 1
   head "https://github.com/boostorg/boost.git"
 
   bottle do
@@ -12,7 +13,7 @@ class BoostMpi < Formula
   end
 
   depends_on "boost"
-  depends_on :mpi => [:cc, :cxx]
+  depends_on "open-mpi"
 
   needs :cxx11