diff --git a/.travis.yml b/.travis.yml index b20eb1875..8c3b9a1b6 100644 --- a/.travis.yml +++ b/.travis.yml @@ -10,8 +10,9 @@ before_install: - conda config --set always_yes yes --set changeps1 no - conda update -q conda - conda info -a - - conda env create -f environment.yml - - source activate augur + - wget http://data.nextstrain.org/nextstrain.yml -O nextstrain.yml; + - conda env create -f nextstrain.yml + - source activate nextstrain install: - pip3 install -e .[dev] script: diff --git a/README.md b/README.md index fa4746cea..7751b5e00 100644 --- a/README.md +++ b/README.md @@ -50,11 +50,12 @@ Augur uses some common external bioinformatics programs which you'll need to ins Alternatively, all these dependencies (as well as augur itself) can be installed via Conda by running: - conda env create -f environment.yml + curl http://data.nextstrain.org/nextstrain.yml --compressed -o nextstrain.yml + conda env create -f nextstrain.yml -Once installed, Conda the enviroment need to be activated whenever augur is to be used, by running: +Once installed, the environment need to be activated whenever augur is to be used, by running: - conda activate augur + conda activate nextstrain ## Usage diff --git a/docs/installation/installation.md b/docs/installation/installation.md index a9d489f51..fd05c0e00 100644 --- a/docs/installation/installation.md +++ b/docs/installation/installation.md @@ -44,13 +44,14 @@ Other Linux distributions will likely have the same packages available, although Alternatively, augur itself and all of its dependencies can be installed into a [Conda](https://conda.io/miniconda.html) environment: - conda env create -f environment.yml + curl http://data.nextstrain.org/nextstrain.yml --compressed -o nextstrain.yml + conda env create -f nextstrain.yml -> _By default this environment is named "augur" but you can change that by providing a name to the above command with `-n `_ +> _By default this environment is named "nextstrain" but you can change that by providing a name to the above command with `-n `_ -When that finishes, the enviroment needs to be activated whenever you want to use augur: +When that finishes, the environment needs to be activated whenever you want to use augur: - conda activate augur + conda activate nextstrain ## Install from source diff --git a/environment.yml b/environment.yml deleted file mode 100644 index e47192005..000000000 --- a/environment.yml +++ /dev/null @@ -1,15 +0,0 @@ -name: augur -channels: -- bioconda -- defaults -dependencies: -- python=3.6 -- mafft -- raxml -- fasttree -- iqtree -- vcftools -- snakemake -- pip -- pip: - - .