Instructions for environment variables.

README.md

@@ -2,15 +2,16 @@
 
 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
@@ -18,3 +19,30 @@ 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 
+   ```