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* 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.
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#!/bin/bash | ||
set -x | ||
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cd src | ||
autoconf | ||
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# build version with MPI & Beagle | ||
./configure \ | ||
--prefix=$PREFIX \ | ||
--disable-debug \ | ||
--with-beagle=$PREFIX \ | ||
--enable-mpi | ||
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make -j$CPU_COUNT | ||
make install | ||
make clean | ||
mv $PREFIX/bin/mb{,-mpi} | ||
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# build version with Beagle only | ||
./configure \ | ||
--prefix=$PREFIX \ | ||
--disable-debug \ | ||
--with-beagle=$PREFIX | ||
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make -j$CPU_COUNT | ||
make install |
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{% set name = "MrBayes" %} | ||
{% set version = "3.2.6" %} | ||
{% set sha256 = "f8fea43b5cb5e24a203a2bb233bfe9f6e7f77af48332f8df20085467cc61496d" %} | ||
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package: | ||
name: {{ name | lower }} | ||
version: {{ version }} | ||
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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 }} | ||
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build: | ||
number: 0 | ||
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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 | ||
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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. |