Updated documentation.

README.md

@@ -4,10 +4,7 @@ A skeleton Git repository for analysis projects.
 # Preparations
 Install dependencies.
 
-```bash
-pip install cookiecutter
-pip install python-gitlab
-```
+    pip install -r https://git.lumc.nl/sasc/cookiecutter-data-analysis/raw/master/requirements.txt
 
 Configure Cookiecutter by editing `.cookiecutterrc` in your home directory.
 
@@ -21,32 +18,26 @@ cookiecutters_dir: /path/to/cookiecutters/
 
 Configure Python GitLab by editing `.python-gitlab.cfg` in your home directory.
 
-```INI
-[global]
-default = gitlab
-ssl_verify = true
-timeout = 5
+    [global]
+    default = gitlab
+    ssl_verify = true
+    timeout = 5
 
-[gitlab]
-url = https://git.lumc.nl
-private_token = your_token_here
-```
+    [gitlab]
+    url = https://git.lumc.nl
+    private_token = your_token_here
 
 # Starting a project
 To start a new analysis project based on this skeleton, use the following
 command.
 
-```bash
-cookiecutter https://git.lumc.nl/sasc/cookiecutter-data-analysis.git
-```
+    cookiecutter https://git.lumc.nl/sasc/cookiecutter-data-analysis.git
 
 ## Working together on the same clone
 If you need to work with other people on the same repository clone on the Shark cluster, you can use the following command to give group access:
 
-```bash
-find -type d -exec chmod 775 {} \;
-find -type f -exec chmod 664 {} \;
-```
+    find -type d -exec chmod 775 {} \;
+    find -type f -exec chmod 664 {} \;
 
 ## Cloning to a portable disk (NTFS)
 Presuming your disk is attached to your own computer and the repository is on

requirements.txt

 cookiecutter
 python-gitlab
-