Merge pull request #146 from sanger-pathogens/travis

Add TravisCI support

.travis.yml

@@ -0,0 +1,22 @@
+language: python
+addons:
+  apt:
+    packages:
+    - autoconf
+    - check
+    - g++
+    - libtool
+    - pkg-config
+    - python-dev
+cache:
+  directories:
+  - "build"
+  - "$HOME/.cache/pip"
+python:
+  - "2.7"
+sudo: false
+install:
+  - "source ./install_dependencies.sh"
+  - "autoreconf -i"
+  - "./configure"
+script: "make check"

install_dependencies.sh

@@ -0,0 +1,111 @@
+#!/bin/bash
+
+set -x
+set -e
+
+start_dir=$(pwd)
+
+RAXML_VERSION="8.1.20"
+FASTML_VERSION="2.3"
+FASTTREE_VERSION="2.1.8"
+
+RAXML_DOWNLOAD_URL="https://github.com/stamatak/standard-RAxML/archive/v${RAXML_VERSION}.tar.gz"
+FASTML_DOWNLOAD_URL="https://github.com/sanger-pathogens/fastml/archive/v${FASTML_VERSION}.tar.gz"
+FASTTREE_DOWNLOAD_URL="http://www.microbesonline.org/fasttree/FastTree-${FASTTREE_VERSION}.c"
+
+# Make an install location
+if [ ! -d 'build' ]; then
+  mkdir build
+fi
+cd build
+build_dir=$(pwd)
+
+# DOWNLOAD ALL THE THINGS
+download () {
+  url=$1
+  download_location=$2
+
+  if [ -e $download_location ]; then
+    echo "Skipping download of $url, $download_location already exists"
+  else
+    echo "Downloading $url to $download_location"
+    wget $url -O $download_location
+  fi
+}
+
+download $RAXML_DOWNLOAD_URL "raxml-${RAXML_VERSION}.tgz"
+download $FASTML_DOWNLOAD_URL "fastml-${FASTML_VERSION}.tgz"
+download $FASTTREE_DOWNLOAD_URL "fasttree-${FASTTREE_VERSION}.c"
+
+# Update dependencies
+if [ "$TRAVIS" = 'true' ]; then
+  echo "Using Travis's apt plugin"
+else
+  sudo apt-get update -q
+  sudo apt-get install -y -q autoconf \
+                             check \
+                             g++ \
+                             libtool \
+                             pkg-config \
+                             python-dev
+fi
+
+# Build all the things
+cd $build_dir
+
+## RAxML
+raxml_dir=$(pwd)/"standard-RAxML-${RAXML_VERSION}"
+if [ ! -d $raxml_dir ]; then
+  tar xzf raxml-${RAXML_VERSION}.tgz
+fi
+cd $raxml_dir
+if [ -e "${raxml_dir}/raxmlHPC" ]; then
+  echo "Already build RAxML; skipping build"
+else
+  make -f Makefile.gcc
+fi
+
+cd $build_dir
+
+## FASTML
+fastml_dir=$(pwd)/"fastml-${FASTML_VERSION}"
+if [ ! -d $fastml_dir ]; then
+  tar xzf fastml-${FASTML_VERSION}.tgz
+fi
+cd $fastml_dir
+if [ -e "${fastml_dir}/programs/fastml/fastml" ]; then
+  echo "Already build FASTML; skipping build"
+else
+  make
+fi
+
+cd $build_dir
+
+## FastTree
+fasttree_dir=${build_dir}/fasttree-${FASTTREE_VERSION}
+if [ ! -d $fasttree_dir ]; then
+  mkdir $fasttree_dir
+fi
+cd $fasttree_dir
+if [ -e "${fasttree_dir}/FastTree" ]; then
+  echo "Skipping, FastTree already exists"
+else
+  gcc -O3 -finline-functions -funroll-loops -Wall -o FastTree ${build_dir}/fasttree-${FASTTREE_VERSION}.c  -lm
+fi
+
+# Setup environment variables
+update_path () {
+  new_dir=$1
+  if [[ ! "$PATH" =~ (^|:)"${new_dir}"(:|$) ]]; then
+    export PATH=${new_dir}:${PATH}
+  fi
+}
+
+update_path ${raxml_dir}
+update_path ${fastml_dir}/programs/fastml
+update_path ${fasttree_dir}
+
+cd $start_dir
+
+set +x
+set +e