From b2aab9f7e06514277763bc17a28320f624607379 Mon Sep 17 00:00:00 2001 From: j23414 Date: Fri, 11 Mar 2022 23:57:10 -0600 Subject: [PATCH 1/3] verbose fix --- .travis.yml | 21 ++++++++++++++++++++- 1 file changed, 20 insertions(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index b7cd372..10d0243 100644 --- a/.travis.yml +++ b/.travis.yml @@ -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 + - 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 + - conda activate nextstrain + - mamba install -c conda-forge -c bioconda augur auspice nextalign snakemake git --yes +# - pip3 install git+https://github.com/nextstrain/cli - nextstrain version - nextstrain check-setup - nextstrain update From 914082adc1c52a4d08b6b94da4437d8d2bddf238 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Mon, 14 Mar 2022 12:50:10 -0500 Subject: [PATCH 2/3] Use the python 3.7 miniconda installer Co-authored-by: Victor Lin <13424970+victorlin@users.noreply.github.com> --- .travis.yml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/.travis.yml b/.travis.yml index 10d0243..9a7c9d7 100644 --- a/.travis.yml +++ b/.travis.yml @@ -8,11 +8,7 @@ before_install: - python3 -m pip install --upgrade pip setuptools wheel install: # 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 + - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; - bash miniconda.sh -b -p $HOME/miniconda - source "$HOME/miniconda/etc/profile.d/conda.sh" - hash -r From 9d587c378c665728bf25cc085add625747c58eef Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Mon, 14 Mar 2022 12:58:52 -0500 Subject: [PATCH 3/3] clean out pip3 install since replaced by mamba Co-authored-by: Victor Lin <13424970+victorlin@users.noreply.github.com> --- .travis.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 9a7c9d7..7a63393 100644 --- a/.travis.yml +++ b/.travis.yml @@ -22,7 +22,6 @@ install: - mamba create -n nextstrain -c bioconda nextstrain-cli --yes - conda activate nextstrain - mamba install -c conda-forge -c bioconda augur auspice nextalign snakemake git --yes -# - pip3 install git+https://github.com/nextstrain/cli - nextstrain version - nextstrain check-setup - nextstrain update