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fix: travis error during installation of dependencies #14

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merged 3 commits into from
Mar 14, 2022
Merged

fix: travis error during installation of dependencies #14

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b2aab9f
verbose fix
Mar 12, 2022
914082a
Use the python 3.7 miniconda installer
Mar 14, 2022
9d587c3
clean out pip3 install since replaced by mamba
Mar 14, 2022
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21 changes: 20 additions & 1 deletion .travis.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,26 @@ python:
before_install:
- python3 -m pip install --upgrade pip setuptools wheel
install:
- pip3 install git+https://github.com/nextstrain/cli
# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/use-conda-with-travis-ci.html#the-travis-yml-file
- if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
else
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
fi
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- bash miniconda.sh -b -p $HOME/miniconda
- source "$HOME/miniconda/etc/profile.d/conda.sh"
- hash -r
- conda config --set always_yes yes --set changeps1 no
- conda update -q conda
# Useful for debugging any issues with conda
- conda info -a
# Install nextstrain cli
- conda install -n base -c conda-forge mamba --yes
- conda activate base
- mamba create -n nextstrain -c bioconda nextstrain-cli --yes
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This would install the latest nextstrain-cli from bioconda rather than latest from the default branch (current behavior with pip3 install git+https://github.com/nextstrain/cli). I think this should be fine though.

- conda activate nextstrain
- mamba install -c conda-forge -c bioconda augur auspice nextalign snakemake git --yes
# - pip3 install git+https://github.com/nextstrain/cli
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- nextstrain version
- nextstrain check-setup
- nextstrain update
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