Instructions for environment variables.

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
+    ```shell
-cd config
+    cd config
-conda env create --file environment.yml
+    conda env create --file environment.yml
-conda activate straw2analysis
+    conda activate straw2analysis
-```
+    ```
-If you have already created this environment, you can update it using:
 
-```shell
+    If you have already created this environment, you can update it using:
-conda deactivate
+
-conda env update --file environment.yml
+    ```shell
-conda activate straw2analysis
+    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 
+   ```