Release 1.0

README.md

@@ -17,9 +17,51 @@ The "gga_load_data" tool is divided in 4 separate scripts:
 - gga_load_data: Load the datasets of the input organisms into their Galaxy library
 - run_workflow_phaeoexplorer: Remotely run a custom workflow in Galaxy, proposed as an "example script" to take inspiration from as workflow parameters are specific to Phaeoexplorer data
 
+## Usage:
+
+The scripts all take one mandatory input file that describes the species and their associated data 
+(see `examples/example.yml`). Every dataset path in this file must be an absolute path.
+
+You must also fill in a config file containing sensitive variables (Galaxy and Tripal passwords, etc..) that
+the script will read to create the different services and to access the Galaxy container. By default, the config file
+inside the repository root will be used if none is precised in the command line. An example of this config file is available
+in the `examples` folder.
+
+**The input file and config file have to be the same for all scripts!**
+
+- Deploy stacks part: 
+
+```bash
+$ python3 /path/to/repo/gga_init.py your_input_file.yml -c/--config your_config_file [-v/--verbose] [OPTIONS]
+		--main-directory $PATH (Path where to create/update stacks; default=current directory)
+		--force-traefik (If specified, will overwrite traefik and authelia files; default=False)
+```
+
+- Copy source data file: 
+
+```bash
+$ python3 /path/to/repo/gga_get_data.py your_input_file.yml [-v/--verbose] [OPTIONS]
+		--main-directory $PATH (Path where to access stacks; default=current directory)
+```
+
+- Load data in Galaxy library and prepare Galaxy instance: 
+
+```bash
+$ python3 /path/to/repo/gga_load_data.py your_input_file.yml -c/--config your_config_file [-v/--verbose]
+		--main-directory $PATH (Path where to access stacks; default=current directory)
+```
+
+- Run a workflow in galaxy: 
+ 
+```bash
+$ 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)
+```
+
 ## Directory tree:
 
-For every input organism, a dedicated directory is created. The script will create this directory and all subdirectories required.
+For every input organism, a dedicated directory is created with `gga_get_data.py`. The script will create this directory and all subdirectories required.
 
 If the user is adding new data to a species (for example adding another strain dataset to the same species), the directory tree will be updated
 
@@ -72,58 +114,18 @@ Directory tree structure:
 
 ```
 
-## Usage:
-
-The scripts all take one mandatory input file that describes the species and their associated data 
-(see `examples/example.yml`). Every dataset path in this file must be an absolute path.
-
-You must also fill in a config file containing sensitive variables (Galaxy and Tripal passwords, etc..) that
-the script will read to create the different services and to access the Galaxy container. By default, the config file
-inside the repository root will be used if none is precised in the command line. An example of this config file is available
-in the `examples` folder.
-
-- Deploy stacks part: 
-
-```bash
-$ python3 /path/to/repo/gga_init.py your_input_file.yml -c/--config your_config_file [-v/--verbose] [OPTIONS]
-		--main-directory $PATH (Path where to create/update stacks; default=current directory)
-		--force-traefik (If specified, will overwrite traefik and authelia files; default=False)
-```
-
-- Copy source data file: 
-
-```bash
-$ python3 /path/to/repo/gga_get_data.py your_input_file.yml [-v/--verbose] [OPTIONS]
-		--main-directory $PATH (Path where to access stacks; default=current directory)
-```
-
-- Load data in Galaxy library and prepare Galaxy instance: 
-
-```bash
-$ python3 /path/to/repo/gga_load_data.py your_input_file.yml -c/--config your_config_file [-v/--verbose]
-		--main-directory $PATH (Path where to access stacks; default=current directory)
-```
-
-- Run a workflow in galaxy: 
- 
-```bash
-$ 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)
-```
-
-**The input file and config file have to be the same for all scripts!**
-
 ## Current limitations
 
-When deploying the stack of services, the Galaxy service can take a long time to be ready. This is due to the Galaxy container preparing a persistent location for the container data. This can be bypassed by setting the variable "persist_galaxy_data" to "False" in the config file.
-
 The stacks deployment and the data loading into Galaxy should hence be run separately and only once the Galaxy service is ready.
 The `gga_load_data.py` script will check that the Galaxy service is ready before loading the data and will exit with a notification if it is not.
 
 You can check the status of the Galaxy service with `$ docker service logs -f genus_species_galaxy` or 
 `./serexec genus_species_galaxy supervisorctl status`.
 
+When deploying the stack of services, the Galaxy service can take a long time to be ready. This is due to the Galaxy container preparing a persistent location for the container data. 
+In development mode only, this can be bypassed by setting the variable "persist_galaxy_data" to "False" in the config file.
+
+
 ## Requirements
 
 Requires Python 3.6