From 471aca45875f2beba30e009e389e4e2ac50c3de6 Mon Sep 17 00:00:00 2001
From: junos <junos.lukan@ijs.si>
Date: Thu, 24 Dec 2020 12:04:22 +0100
Subject: [PATCH] Instructions for environment variables.

---
 README.md | 54 +++++++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 41 insertions(+), 13 deletions(-)

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