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.travis.yml
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.travis.yml
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language: python
sudo: false
env:
- PYTHON_VERSION="3.4"
- PYTHON_VERSION="3.5"
before_install:
- wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
- chmod +x miniconda.sh
- bash miniconda.sh -b -p $HOME/miniconda
- export PATH="$HOME/miniconda/bin:$PATH"
- conda config --set always_yes yes --set changeps1 no
- conda config --add channels https://conda.anaconda.org/biocore
- conda config --add channels https://conda.anaconda.org/mortonjt
- conda update -q conda
- conda info -a
# Install KALIGN
# Install MUSCLE
- wget http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz
- tar zxvf muscle3.8.31_i86linux64.tar.gz
- mkdir muscle
- mv muscle3.8.31_i86linux64 muscle/muscle
- export PATH=$PWD/muscle:$PATH
# Install T-COFFEE
- wget http://www.tcoffee.org/Packages/Stable/Latest/linux/T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.tar.gz
- tar zxvf T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.tar.gz
- export PATH=$PWD/T-COFFEE_installer_Version_11.00.8cbe486_linux_x64/bin:$PATH
# Install TRIMAL
- wget https://github.com/scapella/trimal/archive/v1.4.1.tar.gz
- tar zxvf v1.4.1.tar.gz
- cd trimal-1.4.1/source
- make
- export PATH=$PWD:$PATH
- cd ../..
# Install PHYML
- wget http://www.atgc-montpellier.fr/download/binaries/phyml/PhyML-3.1.zip
- unzip PhyML-3.1.zip
- mv ./PhyML-3.1/PhyML-3.1_linux64 ./PhyML-3.1/phyml
- export PATH=$PWD/PhyML-3.1/phyml:$PATH
# Install MCL
- wget http://micans.org/mcl/src/mcl-14-137.tar.gz
- tar zxvf mcl-14-137.tar.gz
- mkdir mcl-14-137-install
- export MCL_INSTALL_DIR=$PWD/mcl-14-137-install
- cd mcl-14-137
- ./configure --prefix=$MCL_INSTALL_DIR
- make
- make install
- cd ..
- export PATH=$MCL_INSTALL_DIR/bin:$PATH
# Install RANGER
- wget http://compbio.mit.edu/ranger-dtl/ranger-dtl-linux.tar.gz
- tar zxvf ranger-dtl-linux.tar.gz
- export PATH=$PWD/ranger-dtl-linux:$PATH
# Install Java goodies
- mkdir java-files
# Install PhyloNet
- wget http://bioinfo.cs.rice.edu/sites/g/files/bxs266/f/kcfinder/files/PhyloNet_3.5.7.jar -O java-files/PhyloNet_3.5.7.jar --no-check-certificate
install:
# install a few of the dependencies that pip would otherwise try to install
# when intalling scikit-bio
- conda create -n test_env python=$PYTHON_VERSION --file ci/conda_requirements.txt
- source activate test_env
- pip install -r ci/pip_requirements.txt
- pip install .
# Install OrthoFinder (python 3 script, requires before_install dependencies)
- wget https://github.com/ekopylova/OrthoFinder/archive/0.4.python3.tar.gz
- tar zxvf 0.4.python3.tar.gz
- chmod 744 OrthoFinder-0.4.python3/orthofinder.py
- export PATH=$PWD/OrthoFinder-0.4.python3:$PATH
- orthofinder.py --help
script:
- nosetests --with-doctest --with-coverage
- flake8 benchmark/*.py benchmark/tests/*.py distance-method/*.py
after_success:
- coveralls