Update documentation

docs/source/index.md

-## BioInformatics Tool for Infrastructure Automation (BiTIA)
+
+# BioInformatics Tool for Infrastructure Automation (BiTIA)
+
+
 
 
 <p align="center">
@@ -13,28 +16,23 @@
 </p>
 
 
-BiTIA is a tool that simplifies the infrastructure required to run complex bioinformatics pipelines. BiTIA plays well with the existing pipeline solution such as snakement.
+BiTIA is a tool that simplifies the infrastructure required to run complex bioinformatics pipelines. BiTIA plays well with the existing pipeline solution such as snakemake.
+
+BiTIA has two components: **bitia-cli** and **bitita-runner**.
+BiTIA CLI is on the clientside and allows clients to submit tasks to the bitia server.
+BiTIA runner is on the serverside and operates the given tasks to produce results.
 
-BiTIA v1.0 comes with client facing bitia-cli and bitita-runner which manages things at the server end.
+## **bitia-cli**
+Most users only need the `bitia-cli` tool to submit tasks.
+BiTIA CLI creates a zip file of the user input(pipeline) containing a unique hash and ships it to the server.
 
-BiTIA has two components: bitia-cli and bitia-runner.
-- **bitia-cli**
-Creates a zip file of the user input(pipeline) containing a unique hash and ships it to the server.
-- **bitia-runner**
-    Runs the following tasks in the server:
-    - Creates a docker container with the user input
-    - Runs the pipeline
-    - Sends log to the user
-    - Sends link of results(artifacts) to the user
-    - Interacts with common cache for reading data/reference files 
 
 
 [see some examples]: examples
 
 ```{toctree}
-:caption: Getting started
 :hidden: true
-:name: getting_started
+
 
 getting_started/Installation
 getting_started/bioinformatics
@@ -53,15 +51,56 @@ If you want to learn how to use BiTIA and installation, check out the following
 </details>
 <details>
 <summary><b>INSTALLATION</b></summary>
-<div class="termy">
+<<<<<<< HEAD
+
+  To Install BiTIA using pip, run this command:
+  ```{eval-rst}
+  .. tabs::
+
+    .. tab:: Linux
 
-  ```console
-  $ python3 -m  pip install bitia
+           $ python3 -m pip install bitia
 
-  
+    .. tab:: MacOS
+
+           $ python3 -m pip install bitia
+
+
+    .. tab:: Windows
+           
+           $ python3 -m pip install bitia
   ```
-</div>
 </details>
+<details>
+<summary><b>CONFIGURATION</b></summary>
+
+  To Install BiTIA using pip, run this command:
+  ```{eval-rst}
+  .. tabs::
+
+    .. tab:: Linux
+
+           1. `./bitia.toml`  
+           2. `~/.bitia.toml`  
+           3. `$HOME/.config/bitia.toml`  
+           4. `/etc/bitia.toml`  
+
+    .. tab:: MacOS
+
+           1. `./bitia.toml`  
+           2. `~/.bitia.toml`  
+           3. `$HOME/.config/bitia.toml`  
+           4. `/etc/bitia.toml`  
+
+
+    .. tab:: Windows
+           
+           1. `bitia.toml`
+           2. `%APPDATA%\bitia.toml`
+           3. `%PROGRAMDATA%\bitia.toml`
+  ```
+</details>
+
 <details>
 <summary><b>GETTING_STARTED</b></summary>
 
@@ -78,6 +117,7 @@ NGS bioinformatics pipelines are frequently platform specific and may be customi
 </details>
 
 
+
 <details>
 <summary><b>Sequence Alignment</b></summary>
 
@@ -109,12 +149,23 @@ NGS bioinformatics pipelines are frequently platform specific and may be customi
 
 #### Usage Examples
 
+<<<<<<< HEAD
+- **Running Commands**
+```bash
+$ bitia run "samtools foo.fa#https://samtools.github.io/hts-specs/VCFv4.3.pdf"
+```
+The above command will execute 
 
+- **Running Pipeline**
+```bash
+$ bitia run bitia.main.sh
+```
 
 </details>
 
 
 
+
 <!-- 
 ```{eval-rst}
 .. automodule:: bitia