diff --git a/README.md b/README.md index 1eb167f..196c656 100644 --- a/README.md +++ b/README.md @@ -2,19 +2,47 @@ All analysis for the STRAW project. -To install first: +To install: -* Create a conda virtual environment from the `environment.yml` file. +1. Create a conda virtual environment from the `environment.yml` file. -```shell -cd config -conda env create --file environment.yml -conda activate straw2analysis -``` -If you have already created this environment, you can update it using: + ```shell + cd config + conda env create --file environment.yml + conda activate straw2analysis + ``` -```shell -conda deactivate -conda env update --file environment.yml -conda activate straw2analysis -``` \ No newline at end of file + If you have already created this environment, you can update it using: + + ```shell + conda deactivate + conda env update --file environment.yml + conda activate straw2analysis + ``` + +2. Follow [the instructions](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#saving-environment-variables) to set DB_PASSWORD as the environment variable. + + In short, use: + + ```shell + cd $CONDA_PREFIX + mkdir -p ./etc/conda/activate.d + mkdir -p ./etc/conda/deactivate.d + touch ./etc/conda/activate.d/env_vars.sh + touch ./etc/conda/deactivate.d/env_vars.sh + ``` + and then edit `./etc/conda/activate.d/env_vars.sh` as follows: + + ```bash + #!/bin/sh + + export DB_PASSWORD='database-password' + ``` + + and `./etc/conda/deactivate.d/env_vars.sh` as follows: + + ```bash + #!/bin/sh + + unset DB_PASSWORD + ``` \ No newline at end of file