tgvaughan

[alias]
	l = log --graph --pretty=\"%C(auto)%h %C(green)%<(10,trunc)%an%C(auto)%d%Creset %s %C(magenta)(%ar)%Creset\"
	la = log --graph --all --pretty=\"%C(auto)%h %C(green)%<(10,trunc)%an%C(auto)%d%Creset %s %C(magenta)(%ar)%Creset\"
	dw = diff --patience --word-diff

tgvaughan

FROM debian:latest

RUN apt-get update

# Essential build environment
RUN apt-get install -y build-essential git

# Install ruby and bundler
RUN apt-get install -y ruby ruby-dev
RUN gem install bundler

tgvaughan

@printf "BEAGLE version %s\n" bytestring(ccall((:beagleGetVersion,"libhmsbeagle"), Ptr{Cchar}, (),))

@printf "%s\n" bytestring(ccall((:beagleGetCitation,"libhmsbeagle"), Ptr{Cchar}, (),))

#typealias Cint Int64

const BEAGLE_OP_COUNT = 7
const BEAGLE_OP_NONE = -1

tgvaughan

<beast version='2.0'
       namespace='beast.app.beauti:beast.core:beast.evolution.branchratemodel:beast.evolution.speciation:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood:beast.evolution:beast.math.distributions'
       templateinfo='template for structured coalescent analyses'>

       <map name='connect' reserved='true'>beast.app.beauti.BeautiConnector</map>
       <map name='subtemplate' reserved='true'>beast.app.beauti.BeautiSubTemplate</map>

       <beauticonfig spec='BeautiConfig'>

        <panel spec='BeautiPanelConfig' panelname="Partitions" tiptext="Data Partitions"

tgvaughan

traits  time
TREESPARROW_HENAN_1_2004        1
HUMAN_VIETNAM_CL105_2005        2
TREESPARROW_HENAN_4_2004        3
CHICKEN_HEBEI_326_2005  4
CHICKEN_HONGKONG_915_1997       5
VIETNAM_3062_2004       6
GOOSE_HONGKONG_W355_1997        7
DUCK_HONGKONG_Y283_1997 8
DUCK_VIETNAM_376_2005   9

tgvaughan

<project default="build" basedir=".">

    <!-- Source, JUnit test code and jar library locations. -->
    <property name="src" location="src"/>
    <property name="test" location="test"/>
    <property name="lib" location="lib"/>

    <!-- Location to check for local copy of beast2 repository -->
    <property name="beastDir" location="../beast2"/>