From 94755a5a4dc2463ea1cd2a8bdf0620a06f06873a Mon Sep 17 00:00:00 2001
From: Elmar Pruesse <epruesse@users.noreply.github.com>
Date: Thu, 22 Jun 2017 02:06:06 -0600
Subject: [PATCH] Add MrBayes (#5024)

* Add MrBayes

* Work around missing `ssh` and `rsh` on linux docker

* Run `make clean` between mpi/no-mpi builds

* mpirun test needs `allow-run-as-root` flag for docker

* More trying to get mpirun to comply on the docker image

* Something in bioconda chain breaks `test: requires: - conda`

* Pin readline

* Disable `conda inspect` tests

These seem to be broken in the bioconda toolchain setup. Sometimes it
works, sometimes it doesn't.
---
 recipes/mrbayes/build.sh  | 27 +++++++++++++++++++++
 recipes/mrbayes/meta.yaml | 51 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 78 insertions(+)
 create mode 100644 recipes/mrbayes/build.sh
 create mode 100644 recipes/mrbayes/meta.yaml

diff --git a/recipes/mrbayes/build.sh b/recipes/mrbayes/build.sh
new file mode 100644
index 0000000000000..2ec50985a0edb
--- /dev/null
+++ b/recipes/mrbayes/build.sh
@@ -0,0 +1,27 @@
+#!/bin/bash
+set -x
+
+cd src
+autoconf
+
+# build version with MPI & Beagle
+./configure \
+    --prefix=$PREFIX \
+    --disable-debug \
+    --with-beagle=$PREFIX \
+    --enable-mpi
+
+make -j$CPU_COUNT
+make install
+make clean
+mv $PREFIX/bin/mb{,-mpi}
+
+
+# build version with Beagle only
+./configure \
+    --prefix=$PREFIX \
+    --disable-debug \
+    --with-beagle=$PREFIX
+
+make -j$CPU_COUNT
+make install
diff --git a/recipes/mrbayes/meta.yaml b/recipes/mrbayes/meta.yaml
new file mode 100644
index 0000000000000..e36a72efca395
--- /dev/null
+++ b/recipes/mrbayes/meta.yaml
@@ -0,0 +1,51 @@
+{% set name = "MrBayes" %}
+{% set version = "3.2.6" %}
+{% set sha256 = "f8fea43b5cb5e24a203a2bb233bfe9f6e7f77af48332f8df20085467cc61496d" %}
+
+package:
+  name: {{ name | lower }}
+  version: {{ version }}
+
+source:
+  fn: {{ name | lower }}-{{ version }}.tar.gz
+  url: https://sourceforge.net/projects/{{ name | lower }}/files/{{ name | lower }}/{{ version }}/{{ name | lower }}-{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+
+requirements:
+  build:
+    - gcc   # [linux]
+    - llvm  # [osx]
+    - autoconf
+    - automake
+    - readline 6.*
+    - openmpi
+    - beagle-lib
+  run:
+    - libgcc   # [linux]
+    - readline 6.*
+    - openmpi
+    - beagle-lib
+test:
+# conda inspect rules broken in bioconda toolchain
+#  requirements:
+#    - conda
+  commands:
+#    - conda inspect linkages -p $PREFIX $PKG_NAME  # [linux]
+#    - conda inspect objects -p $PREFIX $PKG_NAME  # [osx]
+    - echo Version | mb
+    - echo Version | mpirun -mca plm_rsh_agent true --allow-run-as-root mb-mpi 
+
+about:
+  home: http://mrbayes.sourceforge.net
+  license: GPLv3
+  license_family: GPL
+  license_file: src/gpl.txt
+  summary: Bayesian Inference of Phylogeny
+  description: |
+    MrBayes is a program for Bayesian inference and model choice across a wide
+    range of phylogenetic and evolutionary models. MrBayes uses Markov chain
+    Monte Carlo (MCMC) methods to estimate the posterior distribution of model
+    parameters.