Release 1.0

README.md

@@ -84,25 +84,33 @@ in the `examples` folder.
 
 - Deploy stacks part: 
 
-```$ python3 /path/to/repo/gga_init.py your_input_file.yml -c/--config your_config_file [-v/--verbose] [OPTIONS]
+```bash
+$ python3 /path/to/repo/gga_init.py your_input_file.yml -c/--config your_config_file [-v/--verbose] [OPTIONS]
 		--main-directory $PATH (Path where to create/update stacks; default=current directory)
-		--force-traefik (If specified, will overwrite traefik and authelia files; default=False)```
+		--force-traefik (If specified, will overwrite traefik and authelia files; default=False)
+```
 
 - Copy source data file: 
 
-```$ python3 /path/to/repo/gga_get_data.py your_input_file.yml [-v/--verbose] [OPTIONS]
-		--main-directory $PATH (Path where to access stacks; default=current directory)```
+```bash
+$ python3 /path/to/repo/gga_get_data.py your_input_file.yml [-v/--verbose] [OPTIONS]
+		--main-directory $PATH (Path where to access stacks; default=current directory)
+```
 
 - Load data in Galaxy library and prepare Galaxy instance: 
 
-```$ python3 /path/to/repo/gga_load_data.py your_input_file.yml -c/--config your_config_file [-v/--verbose]
-		--main-directory $PATH (Path where to access stacks; default=current directory)```
+```bash
+$ python3 /path/to/repo/gga_load_data.py your_input_file.yml -c/--config your_config_file [-v/--verbose]
+		--main-directory $PATH (Path where to access stacks; default=current directory)
+```
 
 - Run a workflow in galaxy: 
  
-```$ python3 /path/to/repo/gga_load_data.py your_input_file.yml -c/--config your_config_file --workflow /path/to/workflow.ga [-v/--verbose] [OPTIONS]
+```bash
+$ python3 /path/to/repo/gga_load_data.py your_input_file.yml -c/--config your_config_file --workflow /path/to/workflow.ga [-v/--verbose] [OPTIONS]
 		--workflow $WORKFLOW (Path to the workflow to run in galaxy. A couple of preset workflows are available in the "workflows" folder of the repository)
-		--main-directory $PATH (Path where to access stacks; default=current directory)```
+		--main-directory $PATH (Path where to access stacks; default=current directory)
+```
 
 **The input file and config file have to be the same for all scripts!**