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|
dist: trusty
sudo: false
git:
depth: 1
language: generic
# Custom definitions
.conditions:
if: &secondary type = cron OR env(SECONDARY) = true
matrix:
include:
# http://www.cpan.org/src/
# X.XX-shrplib is a perl built with -Duseithreads.
# https://docs.travis-ci.com/user/languages/perl/
- language: perl
perl: "5.26-shrplib"
env: CC=gcc-8 CXX=g++-8
# https://docs.travis-ci.com/user/languages/java/
- language: java
jdk: oraclejdk9
env: CC=gcc-6 CXX=g++-6
# https://docs.travis-ci.com/user/languages/python/
- language: python
python: "3.6"
- language: generic
env: CC=clang-3.9 CXX=clang++-3.9 LDFLAGS="-fopenmp=libiomp5"
addons:
apt:
sources:
- ubuntu-toolchain-r-test
- llvm-toolchain-precise-3.9
packages:
- clang-3.9
if: *secondary
- language: generic
# Open MP support is available from clang-3.7.
env: CC=clang-3.7 CXX=clang++-3.7 LDFLAGS="-fopenmp=libiomp5"
addons:
apt:
sources:
- ubuntu-toolchain-r-test
- llvm-toolchain-precise-3.7
packages:
- clang-3.7
if: *secondary
# Test old version of the dependency packages.
- language: perl
perl: "5.18-shrplib"
env: BOWTIE2_VERSION=2.2.6
if: *secondary
# https://docs.travis-ci.com/user/reference/osx
- os: osx
osx_image: xcode9.4
env: CC=gcc-8 CXX=g++-8
- os: osx
osx_image: xcode9.4
# "clang++" installed by llvm@3.9 instead of "clang++-3.9".
env: CC=clang-3.9 CXX=clang++
if: *secondary
- os: osx
osx_image: xcode9.4
env: CC=clang-3.7 CXX=clang++-3.7
if: *secondary
allow_failures:
- env: BOWTIE2_VERSION=2.2.6
- env: CC=clang-3.7 CXX=clang++-3.7 LDFLAGS="-fopenmp=libiomp5"
- os: osx
env: CC=clang-3.7 CXX=clang++-3.7
fast_finish: true
install:
- |
if [ "${TRAVIS_OS_NAME}" = "linux" ]; then
# https://launchpad.net/~ubuntu-toolchain-r/+archive/ubuntu/test
sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
sudo apt-get update -qq
# Dependency packages for samtools.
sudo apt-get install -qq \
liblzma-dev \
libbz2-dev
if [[ "${CC}" =~ gcc- ]]; then
echo "Installing ${CC}."
sudo apt-get install -qq "${CC}"
fi
if [[ "${CXX}" =~ g\+\+- ]]; then
echo "Installing ${CXX}."
sudo apt-get install -qq "${CXX}"
fi
if [[ "${CC}" =~ clang- ]]; then
echo "Installing ${CC}."
sudo apt-get install -qq "${CC}" libiomp-dev
fi
else
# osx
export HOMEBREW_NO_AUTO_UPDATE=1
if [[ "${CC}" =~ gcc- ]]; then
# Update command line tool to avoid an error:
# "_stdio.h: No such file or directory", when building samtools.
softwareupdate --list
softwareupdate --install "Command Line Tools (macOS High Sierra version 10.13) for Xcode-10.1"
CC_PKG="$(echo "${CC}" | sed -e 's/-/@/')"
echo "Installing ${CC_PKG}."
brew install "${CC_PKG}"
fi
if [[ "${CC}" =~ clang- ]]; then
echo "Installing ${CC}."
CC_VERSION=$(echo "${CC}" | sed -e 's/^clang-//')
brew install "llvm@${CC_VERSION}"
brew install libomp
CC_PREFIX=$(brew --prefix "llvm@${CC_VERSION}")
export PATH="${CC_PREFIX}/bin:$PATH"
export LDFLAGS="-L${CC_PREFIX}/lib -Wl,-rpath,${CC_PREFIX}/lib"
export CPPFLAGS="-I${CC_PREFIX}/include"
fi
fi
- pushd "${HOME}"
# htslib.
# A dependency of samtools.
- wget https://github.com/samtools/htslib/archive/1.9.tar.gz
- mv 1.9.tar.gz htslib-1.9.tar.gz
- tar xzf htslib-1.9.tar.gz
- pushd htslib-1.9
- make
- sudo make install
- popd
# Samtools.
# Install from autoconf to avoid a lib file load error on Trinity unit test.
- wget https://github.com/samtools/samtools/archive/1.9.tar.gz
- mv 1.9.tar.gz samtools-1.9.tar.gz
- tar xzf samtools-1.9.tar.gz
- pushd samtools-1.9
- autoheader
- autoconf -Wno-syntax
- ./configure || (cat config.log; false)
- make
- sudo make install
- popd
- samtools --version
# Bowtie2
- export BOWTIE2_VERSION="${BOWTIE2_VERSION:-2.3.4.1}"
- |
if [ "${TRAVIS_OS_NAME}" = "linux" ]; then
BOWTIE2_OS_NAME="${TRAVIS_OS_NAME}"
else
# osx
BOWTIE2_OS_NAME=macos
fi
- wget https://github.com/BenLangmead/bowtie2/releases/download/v${BOWTIE2_VERSION}/bowtie2-${BOWTIE2_VERSION}-${BOWTIE2_OS_NAME}-x86_64.zip
- unzip bowtie2-${BOWTIE2_VERSION}-${BOWTIE2_OS_NAME}-x86_64.zip
- sudo cp -p bowtie2-${BOWTIE2_VERSION}*/bowtie2* /usr/local/bin/
- bowtie2 --version
# Jellyfish
- export JELLYFISH_VERSION="${JELLYFISH_VERSION:-2.2.10}"
- wget https://github.com/gmarcais/Jellyfish/releases/download/v${JELLYFISH_VERSION}/jellyfish-${JELLYFISH_VERSION}.tar.gz
- tar xzf jellyfish-${JELLYFISH_VERSION}.tar.gz
- pushd jellyfish-${JELLYFISH_VERSION}
- ./configure || (cat config.log; false)
- make
- sudo make install
- popd
- jellyfish --version
# Salmon
- |
if [ "${TRAVIS_OS_NAME}" = "linux" ]; then
export SALMON_VERSION="${SALMON_VERSION:-0.11.2}"
wget https://github.com/COMBINE-lab/salmon/releases/download/v${SALMON_VERSION}/salmon-${SALMON_VERSION}-linux_x86_64.tar.gz
tar xzf salmon-${SALMON_VERSION}-linux_x86_64.tar.gz
sudo ln -s $(pwd)/salmon-${SALMON_VERSION}-linux_x86_64/bin/salmon /usr/local/bin/salmon
else
# osx
# osx binary archive with required shared library files (tbb + libc++).
# https://github.com/COMBINE-lab/salmon/issues/260
wget https://github.com/COMBINE-lab/salmon/files/2284726/salmon-latest_mac_osx_sierra_x86_64.tar.gz
tar xzvf salmon-latest_mac_osx_sierra_x86_64.tar.gz
sudo cp -p salmon-*/bin/salmon /usr/local/bin/salmon
# Check used shared libraries.
otool -L /usr/local/bin/salmon
# Copy the bundled required library files.
sudo cp -p salmon-*/lib/*.{a,dylib} /usr/local/lib/
fi
- salmon --version
# numpy
- sudo pip install numpy
- popd
before_script:
- |
function show_log {
for file in $(find . -name config.log); do
echo "config.log File: ${file}"
cat "${file}"
done
}
- export TRINITY_HOME=`pwd`
- make || (show_log; false)
- make plugins || (show_log; false)
- sudo make install > /dev/null
script:
- make test -C sample_data/test_Trinity_Assembly
|
