diff --git a/README.md b/README.md index 70921f4..13e7ba4 100644 --- a/README.md +++ b/README.md @@ -37,11 +37,12 @@ git clone https://github.com/blab/flu-forecasting.git cd flu-forecasting ``` -Create and activate a conda environment for the pipeline. +Create and activate a Conda environment for Snakemake. +You will use this environment to run the workflow. ```bash -conda env create -f envs/anaconda.python3.yaml -conda activate flu_forecasting +conda create --yes -c conda-forge -c bioconda -n snakemake snakemake +conda activate snakemake ``` ## Quickstart @@ -51,13 +52,13 @@ This will first simulate influenza-like populations and then fit models to those Inspect all steps to be executed by the pipeline with a dryrun. ```bash -snakemake --dryrun --use-conda --config active_builds='simulated_sample_1' +snakemake --dryrun --use-conda --conda-frontend conda --config active_builds='simulated_sample_1' ``` Run the pipeline locally with four jobs (or cores) at once. ```bash -snakemake --use-conda --config active_builds='simulated_sample_1' -j 4 +snakemake --use-conda --conda-frontend conda --config active_builds='simulated_sample_1' -j 4 ``` Always specify a value for `-j`, to limit the number of cores available to the simulator. @@ -255,19 +256,19 @@ These model files contain all information required to fit the HI- and FRA-based Run the entire pipeline locally with four simultaneous jobs. ```bash -snakemake --use-conda -j 4 +snakemake --use-conda --conda-frontend conda -j 4 ``` You can also run just one of the natural builds as follows, to confirm your environment is configured properly. ```bash -snakemake --use-conda --config active_builds='natural_sample_1_with_90_vpm_sliding' -j 4 +snakemake --use-conda --conda-frontend conda --config active_builds='natural_sample_1_with_90_vpm_sliding' -j 4 ``` Or you can run just one of the simulated builds as follows. ```bash -snakemake --use-conda --config active_builds='simulated_sample_3' -j 4 +snakemake --use-conda --conda-frontend conda --config active_builds='simulated_sample_3' -j 4 ``` Alternately, follow [Snakemake documentation to distribute the entire pipeline to your cloud or cluster accounts](https://snakemake.readthedocs.io/en/stable/executing/cluster-cloud.html). diff --git a/envs/anaconda.python3.yaml b/envs/anaconda.python3.yaml index 8af20b7..39c82d0 100644 --- a/envs/anaconda.python3.yaml +++ b/envs/anaconda.python3.yaml @@ -1,5 +1,6 @@ name: flu_forecasting channels: +- conda-forge - bioconda - defaults dependencies: