More contents for "local setup"

docs/source/conf.py

@@ -75,8 +75,10 @@ source_suffix = {
 }
 
 # To enable AutoStructify: https://github.com/readthedocs/recommonmark#autostructify
+#github_doc_root = 'https://github.com/Xuqian-Yan/nexuse-doc/docs/'
 def setup(app):
     app.add_config_value('recommonmark_config', {
+#            'url_resolver': lambda url: github_doc_root + url,
             'enable_eval_rst': True,
             }, True)
     app.add_transform(AutoStructify)

docs/source/setup.md

@@ -2,14 +2,15 @@
 
 - [Get permissions](#get-permissions)
 - [Local setup](#local-setup)
+  - [Get the codes](#get-the-codes)
+  - [Prepare software & license](#prepare-software-license)
 - [Euler setup](#euler-setup)
 
 #### Get permissions
 
 Before setting up, you need permissions to access the codes and the input database. Email the following people to ask for the corresponding permissions.
 
-```eval_rst
-|:warning:| **NOTE**: Currently, the codes are only accessble with an ETH account.
+```Note:: |:warning:| Currently, the codes are only accessible with an ETH account.
 ```
 
 - Xuejiao Han (xuhan@eeh.ee.ethz.ch): 
@@ -28,14 +29,65 @@ Before setting up, you need permissions to access the codes and the input databa
 - Florian Landis  (landisf@ethz.ch):
   - permission for the **GemEl** repository
 - Xuqian Yan (xuqian.yan@esc.ethz.ch):
-  - permission for the overarching **Nexus-e** repository
+  - permission for the overarching **Nexus-e** repository (<https://gitlab.ethz.ch/xyan/nexus-e.git>)
 
 #### Local setup
 
-1. Get the codes
-1. Prepare software & license
-1. Connect with the input database
-1. Run Nexus-e
+Most the instructions below have been tested both on **Windows** and on **Mac**.
+
+#####  1. Get the codes
+
+The instructions here use **command lines**. If you have a GUI tool for git, you could use the corresponding operations in the GUI tool instead. An example using a GUI tool "GitAhead" can be found in section [Nexus-e repository instructions](nexuse_repo_instruction.html).
+
+- Create a folder where you want to put the codes
+
+- cd to that folder
+
+- Clone the overarching repository with this command:
+
+  ```git clone --recursive https://gitlab.ethz.ch/xyan/nexus-e.git```
+
+  You will be asked for your username and password for the repository and its submodules. Input your ETH username and password.
+
+In the end, the folder will look like this:
+
+![](images/nexus-e-folder.png)
+
+
+##### 2. Connect with the input database
+
+
+##### 3. Prepare software & license
+
+- Matlab (2018a or higher)
+
+  - Set up database connector
+
+    - Download the **MySQL connector** from [here](https://dev.mysql.com/downloads/connector/j/).  
+    Or, if you have access to the Nexus-e polybox, use the `mysql-connector-java-8.0.18.zip` provided in the folder `02_Model/02_02_Model_Setup_Instruction`(**Unzip** the file before the next step).
+
+    - Copy the MySQL connector folder (e.g. mysql-connector-java-8.0.18) into a folder at your preference.  
+    We recommend to put it into the **Matlab preferences folder**, which you can find by typing in Matlab Command Window ```prefdir```.
+
+    - Create a **javaclasspath.txt** file in the **Matlab preferences folder**.
+
+    - In the **javaclasspath.txt** file, put the path to the connector .jar file.  
+    E.g., On Blazhe's Windows computer the path is `C:\Users\gblazhe\AppData\Roaming\MathWorks\MATLAB\R2018a\mysql-connector-java-8.0.18\mysql-connector-java-8.0.18.jar`.
+
+    - Reload Matlab
+    
+    - Test whether a database connector is set up successfully. Write the following commands in Matlab (substitue `YOUR_USERNAME` and `YOUR_PASSWORD` with your credentials for the database). If the second command returns `1`, it means success.  
+    ```
+    conn = database("sys", YOUR_USERNAME, YOUR_PASSWORD, 'Vendor', 'MySQL', 'Server', "itet-psl-s02");
+    isopen(conn)
+    ```
+      
+    
+
+- 
+
+
+##### 4. Run Nexus-e
 
 #### Euler setup
 1. Join the usergroup