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.travis.yml
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.travis.yml
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sudo: required
language: python
python: '3.7'
cache: pip
matrix:
fast_finish: true
before_install:
# install conda
- wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
- chmod +x miniconda.sh
- ./miniconda.sh -b
- export PATH=/home/travis/miniconda2/bin:$PATH
- conda update --yes conda
install:
# use the conda env to install all dependencies
- mkdir -p /tmp/conda
- conda env create -p /tmp/conda/hicpro -f environment.yml
- export PATH=/tmp/conda/hicpro/bin:$PATH
# Install HiC-Pro
- mkdir /tmp/apps
- make configure prefix=/tmp/apps
- make install
script:
# Get test data
- mkdir -p $HOME/test-op && cd $HOME/test-op
- wget https://zerkalo.curie.fr/partage/HiC-Pro/hicpro_testop_travis.tar.gz -P $HOME/test-op/ && tar -zxvf hicpro_testop_travis.tar.gz
- /bin/rm -f hicpro_testop_travis.tar.gz
# Run HiC-Pro
- INSTALLED_HICPRO_VERSION=$(find /tmp/apps -name HiC-Pro | xargs dirname)
- time $INSTALLED_HICPRO_VERSION/HiC-Pro -i test_data -o $HOME/test-op/results -c config_testop_yeast.txt