diff --git a/README.md b/README.md
index 590e82bd6faff6e535e1511477f36f7209698f36..144f85d5aae7eaa02980313aba48df694a76cf94 100755
--- a/README.md
+++ b/README.md
@@ -75,11 +75,23 @@ Directory tree structure:
 ```
 
 ## Steps:
-For each input organism:
+For each input organism, the tool works in three parts (1 part = 1 separate script).
+
+**The first two parts are required to set up a functional GGA stack**
+
+**Part 1)**
 1) Create the directory tree structure (if it already exists, only create the required subdirectories)
-2) Create the dockerfile for the organism and deploy the stack of services. If the dockerfile exists, skips this step
+2) Create the docker-compose file for the organism and deploy the stack of services.
+
+
+**Warning: the Galaxy service takes up to 2 hours to be set up. During these 2 hours it can't be interacted with, wait at least 2 hours 
+before calling the other scripts**
+
+**Part 2)**
 3) Gather source data files as specified in the input, can recursively search the directory (fully automated for local phaeoexplorer data)
-4) Link the source files to the organism correct src_data folders
+4) Link the source files to the organism correct src_data folders and load the data into the galaxy container
+
+*(Optional)* **Part 3)**
 5) (*Optional*) Modify headers in the transcripts and protein fasta files
 6) (*Optional*) TODO: Generate blast banks (no commit)
 7) (*Optional*) Connect to the galaxy instance
@@ -87,7 +99,13 @@ For each input organism:
 9) (*Optional*) TODO: Generate and update metadata files
 
 ## Usage:
-```WIP```
+- Deploy stacks part: ```$ python3 /path/to/repo/deploy_stacks.py -i your_input_file.yml```
+
+- Copy source data file and load data into the galaxy container: ```$ python3 /path/to/repo/load_data.py -i your_input_file.yml```
+
+- Run a workflow: ```$ python3 /path/to/repo/run_workflow.py -i your_input_file.yml``` 
+
+**Warning: the input file have to be the same for the 3 steps!**
 
 ## Current limitations
 When deploying the stack of services, the galaxy service takes a long time to be ready (around 2 hours of wait time).
@@ -97,6 +115,9 @@ For the moment, the stacks deployment and the data loading into galaxy should be
 To check the status of the galaxy service, run ```$ docker service logs -f genus_species_galaxy```
 
 ## Requirements (*temporary*):
+Requires Python 3.7+
+
+Packages required:
 ```
 bioblend==0.14.0  
 boto==2.49.0
diff --git a/create_input_instance.py b/create_input_instance.py
new file mode 100644
index 0000000000000000000000000000000000000000..9ef50aaff9db6a5111f59dceaae63bf24616f220
--- /dev/null
+++ b/create_input_instance.py
@@ -0,0 +1,161 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+
+import argparse
+import os
+import logging
+import sys
+import json
+import yaml
+import re
+from datetime import datetime
+
+"""
+create_input_instance.py
+
+Create an object containing the data input from the yml file as attributes
+This object is then fed to the other scripts
+It is to avoid having several times the same code in several files
+
+"""
+
+
+def parse_input(input_file):
+    """
+    Parse the yml input file to extract data to create the SpeciesData objects
+    Return a list of dictionaries. Each dictionary contains all the data
+
+    :param input_file:
+    :return:
+    """
+
+    parsed_sp_dict_list = []
+
+    if str(input_file).endswith("yml") or str(input_file).endswith("yaml"):
+        logging.debug("Input format used: YAML")
+    else:
+        logging.critical("Error, please input a YAML file")
+        sys.exit()
+    with open(input_file, 'r') as stream:
+        try:
+            yaml_dict = yaml.safe_load(stream)
+            for k, v in yaml_dict.items():
+                parsed_sp_dict_list.append(v)
+        except yaml.YAMLError as exc:
+            logging.debug(exc)
+    return parsed_sp_dict_list
+
+
+
+
+class SpeciesData:
+    """
+    This class contains attributes and functions to interact with the galaxy container of the GGA environment
+
+
+    """
+
+    def __init__(self, parameters_dictionary, args):
+        self.parameters_dictionary = parameters_dictionary
+        self.args = args
+        self.species = parameters_dictionary["description"]["species"]
+        self.genus = parameters_dictionary["description"]["genus"]
+        self.strain = parameters_dictionary["description"]["strain"]
+        self.sex = parameters_dictionary["description"]["sex"]
+        self.common = parameters_dictionary["description"]["common_name"]
+        self.date = datetime.today().strftime("%Y-%m-%d")
+        self.origin = parameters_dictionary["description"]["origin"]
+        self.performed = parameters_dictionary["data"]["performed_by"]
+        if parameters_dictionary["data"]["genome_version"] == "":
+            self.genome_version = "1.0"
+        else:
+            self.genome_version = parameters_dictionary["data"]["genome_version"]
+        if parameters_dictionary["data"]["ogs_version"] == "":
+            self.ogs_version = "1.0"
+        else:
+            self.ogs_version = parameters_dictionary["data"]["ogs_version"]
+        self.genus_lowercase = self.genus[0].lower() + self.genus[1:]
+        self.genus_uppercase = self.genus[0].upper() + self.genus[1:]
+        self.species_folder_name = "_".join([self.genus_lowercase, self.species, self.strain, self.sex])
+        self.full_name = " ".join([self.genus_uppercase, self.species, self.strain, self.sex])
+        self.abbreviation = " ".join([self.genus_lowercase[0], self.species, self.strain, self.sex])
+        self.genus_species = self.genus_lowercase + "_" + self.species
+        self.instance_url = "http://scratchgmodv1:8888/sp/" + self.genus_lowercase + "_" + self.species + "/galaxy/"  # Testing with localhost/scratchgmodv1
+        self.instance = None
+        self.history_id = None
+        self.library_id = None
+        self.script_dir = os.path.dirname(os.path.realpath(sys.argv[0]))
+        self.main_dir = None
+        self.species_dir = None
+        self.org_id = None
+        self.genome_analysis_id = None
+        self.ogs_analysis_id = None
+        self.tool_panel = None
+        self.datasets = dict()
+        self.source_files = dict()
+        self.workflow_name = None
+        self.docker_compose_generator = None
+        self.metadata = dict()
+        self.api_key = "dev"  # TODO: set the key in config file --> saved for later (master api key access actions are limited)
+        if parameters_dictionary["data"]["parent_directory"] == "" or parameters_dictionary["data"]["parent_directory"] == "/path/to/closest/parent/dir":
+            self.source_data_dir = "/projet/sbr/phaeoexplorer/"  # Testing path for phaeoexplorer data
+        else:
+            self.source_data_dir = parameters_dictionary["data"]["parent_directory"]
+        # Directory/subdirectories where data files are located (fasta, gff, ...), point to a directory as close as possible to the source files
+        self.do_update = False  # Update the instance (in histories corresponding to the input) instead of creating a new one // TODO: move this variable inside methods
+        self.api_key = "dev"  # API key used to communicate with the galaxy instance. Set to "dev" for the moment. Cannot be used to do user-tied actions
+        self.args = args
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Automatic data loading in containers and interaction with galaxy instances for GGA"
+                                                 ", following the protocol @ "
+                                                 "http://gitlab.sb-roscoff.fr/abims/e-infra/gga")
+
+    # Dev arguments, TODO: remove in production branch!
+    parser.add_argument("--full",
+                        help="Run everything, from src_data dir tree creation, moving data files (abims) into src_data,"
+                             "modify headers (abims), generate blast banks (doesn't commit them: TODO), initialize GGA instance, load the data and run,"
+                             " the main workflow. To update/add data to container, use --update in conjunction to --full (TODO)")
+
+    parser.add_argument("--init-instance",
+                        help="Initialization of galaxy instance. Run first in an empty instance, DEV",
+                        action="store_true")
+
+    parser.add_argument("--deploy-stacks",
+                        help="Create and deploy the stacks of services",
+                        action="store_true")
+
+    parser.add_argument("--load-data",
+                        help="Create src_data directory tree, copy datasets to src_data, and load these datasets into the instance, DEV",
+                        action="store_true")
+
+    parser.add_argument("--run-workflow",
+                        help="Run main workflow (load data into chado, sync all with tripal, "
+                             "index tripal data, populate materialized view, "
+                             "create a jbrowse for the current genus_species_strain_sex and add organism to jbrowse")
+
+
+    # Production arguments
+    parser.add_argument("input", type=str, help="Input file (yml)")
+
+    parser.add_argument("-v", "--verbose",
+                        help="Increase output verbosity",
+                        action="store_false")
+
+    parser.add_argument("--update",
+                        help="Update an already integrated organisms with new data from input file, docker-compose.yml will not be re-generated"
+                             ", assuming the instances for the organisms are already generated and initialized",
+                        action="store_false")
+
+    parser.add_argument("--dir",
+                        help="Path of the main directory, either absolute or relative, defaults to current directory",
+                        default=os.getcwd())
+
+    args = parser.parse_args()
+
+    if args.verbose:
+        logging.basicConfig(level=logging.DEBUG)
+    else:
+        logging.basicConfig(level=logging.INFO)
+
+
diff --git a/deploy.sh b/deploy.sh
index 16f4a33a0dfbae5c84ffd614a0ea9db0942484a1..784000e28096e9b107ebaa5e95f49e6bcc1ddee0 100755
--- a/deploy.sh
+++ b/deploy.sh
@@ -11,8 +11,10 @@ cd ..
 
 if docker network ls | grep -q 'traefik'
 then
+    cd $1
     docker stack deploy -c docker-compose.yml $1
 else
+    cd $1
     docker stack deploy -c docker-compose.yml $1
 fi
 
diff --git a/deploy_stacks.py b/deploy_stacks.py
index 86a87b614c86c2143b63d8435a029f0c55581b14..73b766e502cd646361b7bacd1b1d6d281e0fccba 100755
--- a/deploy_stacks.py
+++ b/deploy_stacks.py
@@ -1,4 +1,5 @@
-#!/usr/bin/env python3
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
 
 import bioblend
 import bioblend.galaxy.objects
@@ -17,26 +18,19 @@ import table_parser
 import fnmatch
 import shutil
 from datetime import datetime
+import create_input_instance
+
+""" 
+deploy_stacks.py
+
 
-"""
-gga_load_data main script
-    
-Scripted integration of new data into GGA instances. The input is either a table-like (csv, xls, ...) or a json (TODO: yaml) file
-that describes what data is to be integrated (genus, species, sex, strain, data), see data_example.json for an example of the correct syntax.
-The script will parse the input and take care of everything, from source files directory tree creation to running the gmod tools
-inside the galaxy instances of organisms. 
-
-By default, the script will do everything needed to have a functional instance from scratch. If you want to bypass this behavior, 
-you have to specify --update as a parameter. The script can also be used to update an existing GGA instance with new data. For example, you have an instance "genus_species" 
-with data for the male sex and want to add the female sex to the same GGA instance. To do this, create your configuration input file as you would normally, and add the "--update"
-argument when invoking the script.
 
 TODO:
 - add config file (inside repo or outside with argument
 - update existing history
-- clean/delete instance
-- delete stack
-- commit the files for blast banks
+- clean/delete instance?
+- delete stack?
+- commit the files for blast banks.
 
 TODO EOSC/Cloudification:
 - divide into 2 general-use scripts
@@ -57,7 +51,7 @@ STEPS:
 
 NOTES:
 - A master API key cannot be used, as some functions are tied to a user (like creating an history), so the access to the
-  galaxy instance must be done using email and password
+  galaxy instance must be done using email and password (definable in yml_example_input.yml)
 
 """
 
@@ -87,9 +81,11 @@ def parse_input(input_file):
     return parsed_sp_dict_list
 
 
-class Autoload:
+
+
+class DeploySpeciesStacks:
     """
-    The "Autoload" class contains attributes and functions to interact with the galaxy container of the GGA environment
+    The class DeploySpeciesStacks
 
 
     """
@@ -116,7 +112,7 @@ class Autoload:
         self.genus_lowercase = self.genus[0].lower() + self.genus[1:]
         self.genus_uppercase = self.genus[0].upper() + self.genus[1:]
         self.species_folder_name = "_".join([self.genus_lowercase, self.species, self.strain, self.sex])
-        self.full_name = " ".join([self.genus_lowercase, self.species, self.strain, self.sex])
+        self.full_name = " ".join([self.genus_uppercase, self.species, self.strain, self.sex])
         self.abbreviation = " ".join([self.genus_lowercase[0], self.species, self.strain, self.sex])
         self.genus_species = self.genus_lowercase + "_" + self.species
         self.instance_url = "http://scratchgmodv1:8888/sp/" + self.genus_lowercase + "_" + self.species + "/galaxy/"  # Testing with localhost/scratchgmodv1
@@ -177,6 +173,9 @@ class Autoload:
     #             if self.species and self.sex in f:
     #                 logging.info("File found")
 
+
+
+
     def generate_dir_tree(self):
         """
         Generate the directory tree for an organism and move datasets into src_data
@@ -251,7 +250,7 @@ class Autoload:
             for line in infile:
                 # One-liner to replace placeholders by the genus and species
                 organism_content.append(
-                    line.replace("genus_species", str(self.genus.lower() + "_" + self.species)).replace("Genus species", str(self.genus + " " + self.species)).replace("Genus/species", str(self.genus + "/" + self.species)).replace("gspecies", str( self.genus.lower()[0] + self.species)).replace("genus_species_strain_sex", genus_species_strain_sex))
+                    line.replace("genus_species", str(self.genus.lower() + "_" + self.species)).replace("Genus species", str(self.genus_uppercase + " " + self.species)).replace("Genus/species", str(self.genus_uppercase + "/" + self.species)).replace("gspecies", str( self.genus.lower()[0] + self.species)).replace("genus_species_strain_sex", genus_species_strain_sex))
             with open("./docker-compose.yml", 'w') as outfile:
                 for line in organism_content:
                     outfile.write(line)
@@ -271,7 +270,9 @@ class Autoload:
             logging.debug("Traefik compose file already exists")
         subprocess.call(["python3", self.script_dir + "/create_mounts.py"], cwd=working_dir)
 
-    def get_source_data_files(self):
+
+
+    def get_source_data_files_from_path(self):
         """
         Find all files in source_data directory, to link the matching files in the src_data dir tree
 
@@ -320,6 +321,8 @@ class Autoload:
                         except NotADirectoryError:
                             logging.warning("Error raised (NotADirectoryError)")
 
+
+
     def deploy_stack(self):
         """
         Call the script "deploy.sh" used to initiliaze the swarm cluster if needed and launch/update the stack
@@ -330,6 +333,10 @@ class Autoload:
         # TODO: add a fail condition?
         subprocess.call(["sh", self.script_dir + "/deploy.sh", self.genus_species, self.main_dir + "/traefik"])
 
+
+
+
+
     def modify_fasta_headers(self):
         """
         Change the fasta headers before integration.
@@ -393,44 +400,27 @@ class Autoload:
                            stdout=subprocess.PIPE,
                            cwd=annotation_dir)
 
-    def generate_blast_banks(self):
-        """
-        TODO
-        Automatically generate blast banks for a species
-        TODO: auto commit the files?
 
-        :return:
-        """
 
-    # @commit_files
-    def generate_blast_banks_and_commit(self):
-        """
-        TODO
-
-        :return:
-        """
-        return None
 
-    def commit_files(self):
+    def generate_blast_banks(self):
         """
         TODO
-        Commit files to a git repo
-        Commits to the gga repo for phaeoexplorer
-        TODO: add repo to config file
+        Automatically generate blast banks for a species
+        TODO: auto commit the files?
 
         :return:
         """
 
-        return None
 
     def connect_to_instance(self):
         """
         TODO: move in init/access
-
+        TODO: password
         Test the connection to the galaxy instance for the current organism
         Exit if it cannot connect to the instance
         """
-        self.instance = galaxy.GalaxyInstance(url=self.instance_url, email="admin@galaxy.org", password="password", verify=False)
+        self.instance = galaxy.GalaxyInstance(url=self.instance_url, email="gga@sb-roscoff.fr", password="password", verify=False)
         logging.info("Connecting to the galaxy instance ...")
         try:
             self.instance.histories.get_histories()
@@ -440,7 +430,11 @@ class Autoload:
             sys.exit()
         else:
             logging.info("Successfully connected to galaxy instance @ " + self.instance_url)
-        self.instance.histories.create_history(name=str(self.full_name))
+        self.instance.histories.create_history(name="FOO")
+
+
+
+
 
 
     def setup_data_libraries(self):
@@ -470,6 +464,10 @@ class Autoload:
         # self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["transcripts_file"])
         # self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["proteins_file"])
 
+
+
+
+
     def get_species_history_id(self):
         """
         Set and return the current species history id in its galaxy instance
@@ -482,13 +480,20 @@ class Autoload:
 
         return self.history_id
 
+
+
+
     def create_species_history(self):
         histories = self.instance.histories.get_histories(name=str(self.full_name))
         print("\n" + str(histories) + "\n" + self.full_name + "\n")
         if not histories:
-            self.instance.histories.create_history(name=str(self.full_name))
+            self.instance.histories.create_history(name="FOO")
             print("Created history!")
 
+
+
+
+
     def get_instance_attributes(self):
         """
         retrieves instance attributes:
@@ -546,6 +551,11 @@ class Autoload:
                                 self.datasets["gff_file"] = e["ldda_id"]
                                 logging.info("\t\t" + e["name"] + ": " + e["ldda_id"])
 
+
+
+
+
+
     def init_instance(self):
         """
         Galaxy instance startup in preparation for running workflows
@@ -627,6 +637,12 @@ class Autoload:
         self.get_organism_and_analyses_ids()
         logging.info("Finished initializing instance")
 
+
+
+
+
+
+
     def run_workflow(self, workflow_name, workflow_parameters, datamap):
         """
         Run the "main" workflow in the galaxy instance
@@ -686,6 +702,11 @@ class Autoload:
                                                     inputs_by="")
             self.instance.workflows.delete_workflow(workflow_id=workflow_id)
 
+
+
+
+
+
     def load_data_in_galaxy(self):
         """
         Function to load the src_data folder in galaxy
@@ -697,6 +718,10 @@ class Autoload:
 
         return None
 
+
+
+
+
     def get_organism_and_analyses_ids(self):
         """
         Retrieve current organism ID and OGS and genome chado analyses IDs (needed to run some tools as Tripal/Chado
@@ -743,6 +768,9 @@ class Autoload:
         except IndexError:
             logging.debug("no matching genome analysis exists in the instance's chado database")
 
+
+
+
     def clean_instance(self):
         """
         TODO: method to purge the instance from analyses and organisms
@@ -751,6 +779,9 @@ class Autoload:
         return None
 
 
+
+
+
 def filter_empty_not_empty_items(li):
     ret = {"empty": [], "not_empty": []}
     for i in li:
@@ -812,18 +843,21 @@ if __name__ == "__main__":
         al = Autoload(parameters_dictionary=sp_dict, args=args)
         al.main_dir = os.path.abspath(args.dir)
         if args.load_data:
-
-            al.generate_dir_tree()
-            logging.info("Successfully generated the directory tree for " + al.genus[0].upper() + ". " + al.species + " " + al.strain + " " + al.sex)
-
-            al.get_source_data_files()
-            logging.info("Successfully retrieved source data files for " + al.genus[0].upper() + ". " + al.species + " " + al.strain + " " + al.sex)
-
-            al.deploy_stack()
-            logging.info("Successfully deployed containers stack for " + al.genus[0].upper() + ". " + al.species + " " + al.strain + " " + al.sex)
-
-            # al.connect_to_instance()
-            # logging.info("Connected to instance")
+            """
+            Full workflow 
+            TODO: change later (docker side / load data side / galaxy side)
+            """
+            # al.generate_dir_tree()
+            # logging.info("Successfully generated the directory tree for " + al.genus[0].upper() + ". " + al.species + " " + al.strain + " " + al.sex)
+            #
+            # # al.get_source_data_files_from_path()
+            # logging.info("Successfully retrieved source data files for " + al.genus[0].upper() + ". " + al.species + " " + al.strain + " " + al.sex)
+            #
+            # al.deploy_stack()
+            # logging.info("Successfully deployed containers stack for " + al.genus[0].upper() + ". " + al.species + " " + al.strain + " " + al.sex)
+            #
+            al.connect_to_instance()
+            logging.info("Connected to instance")
             #
             # al.create_species_history()
             # logging.info("Created a history")
@@ -883,3 +917,13 @@ if __name__ == "__main__":
             #     print(al.species_dir)
 
     logging.info("Exit")
+
+
+
+def main(species_data):
+    """
+    "Main" function
+
+    :return:
+    """
+    print("OK")
\ No newline at end of file
diff --git a/examples/example.json b/examples/example_input.json
similarity index 96%
rename from examples/example.json
rename to examples/example_input.json
index 843ed64c8696fe2488a2d024460a683bc9a96ee2..669bc8846ae237e6a2d21af8df7f1190ff38a5c4 100755
--- a/examples/example.json
+++ b/examples/example_input.json
@@ -1,28 +1,28 @@
-[
-    {
-        "genus" : "genus1",
-        "species" : "Species1",
-        "common" : "Common1",
-        "strain" : "strain1",
-        "sex" : "male",
-        "origin" : "Unknown",
-        "version" : "1.0",
-        "performed by" : "Institute John Doe",
-        "genome version" : "1.0",
-        "ogs version" : "1.0",
-        "date" : "2020-01-01"
-    },
-    {
-        "genus" : "genus2",
-        "species" : "Species2",
-        "common" : "Common2",
-        "strain" : "strain2",
-        "sex" : "female",
-        "origin" : "Unknown",
-        "version" : "1.0",
-        "performed by" : "Institute Jane Doe",
-        "genome version" : "1.0",
-        "ogs version" : "1.0",
-        "date" : "2020-01-01"
-    }
-]
+[
+    {
+        "genus" : "genus1",
+        "species" : "Species1",
+        "common" : "Common1",
+        "strain" : "strain1",
+        "sex" : "male",
+        "origin" : "Unknown",
+        "version" : "1.0",
+        "performed by" : "Institute John Doe",
+        "genome version" : "1.0",
+        "ogs version" : "1.0",
+        "date" : "2020-01-01"
+    },
+    {
+        "genus" : "genus2",
+        "species" : "Species2",
+        "common" : "Common2",
+        "strain" : "strain2",
+        "sex" : "female",
+        "origin" : "Unknown",
+        "version" : "1.0",
+        "performed by" : "Institute Jane Doe",
+        "genome version" : "1.0",
+        "ogs version" : "1.0",
+        "date" : "2020-01-01"
+    }
+]
diff --git a/examples/phaeoexplorer_test.json b/examples/phaeoexplorer_test.json
deleted file mode 100644
index bd281b978a978105236b25bf6eeb64b290a7406d..0000000000000000000000000000000000000000
--- a/examples/phaeoexplorer_test.json
+++ /dev/null
@@ -1,30 +0,0 @@
-[
-    {
-        "genus" : "Ectocarpus",
-        "species" : "sp1",
-        "common" : "",
-        "strain" : "",
-        "sex" : "male",
-        "origin" : "Unknown",
-        "version" : "1.0",
-        "performed by" : "Genoscope",
-        "genome version" : "1.0",
-        "ogs version" : "1.0",
-        "date" : "2020-08-03"
-    },
-    {
-        "genus" : "Ectocarpus",
-        "species" : "sp2",
-        "common" : "",
-        "strain" : "",
-        "sex" : "male",
-        "origin" : "Unknown",
-        "version" : "1.0",
-        "performed by" : "Genoscope",
-        "genome version" : "1.0",
-        "ogs version" : "1.0",
-        "date" : "2020-08-03"
-    }
-]
-
-
diff --git a/examples/example.xlsx b/examples/xlsx_example_input.xlsx
similarity index 100%
rename from examples/example.xlsx
rename to examples/xlsx_example_input.xlsx
diff --git a/examples/example.yml b/examples/yml_example_input.yml
similarity index 80%
rename from examples/example.yml
rename to examples/yml_example_input.yml
index ff066611da17cfc7bbe7a1fbbf4a35610e5552d6..af0fe1213e1ac36cd0011d8bf74cbe6097f74c20 100644
--- a/examples/example.yml
+++ b/examples/yml_example_input.yml
@@ -1,5 +1,15 @@
 # Config file for the automated creation GGA docker stacks
-# The file consists in a list of species for which the script will have to create stacks and load data into galaxy
+# The file consists in a small configurable set of users + passwords for the the stacks and a
+# list of species for which the script will have to create these stacks/load data into galaxy/run workflows
+# Add new config option using a config scalar
+
+
+config:  # Simple config part, allowing the user to create his/her own admin account (default is gga)
+  # WARNING: not supported currently, as the default connection is using the gga account
+  admin:
+    username: "nflantier"  # Desired admin username
+    password: "blanquette"  # Desired admin password
+    email: "noel.flantier@galaxy.org"  # Desired admin email
 
 ectocarpus_sp1:  # Dummy value the user gives to designate the species (isn't used by the script)
   # Species description, leave blank if unknown or you don't want it to be used
@@ -12,7 +22,7 @@ ectocarpus_sp1:  # Dummy value the user gives to designate the species (isn't us
     strain: ""
     common_name: ""
     origin: ""
-  # Data files.
+  # Data files scalars contain paths to the source files that have to be loaded into galaxy
   # WARNING: The paths must be absolute paths!
   # If any path is left blank and the "parent_directory" scalar is specified, this directory and ALL its subdirectories will be
   # scanned for files corresponding to the description provided for the species (i.e if the user specified
@@ -57,4 +67,3 @@ ectocarpus_sp2:
     genome_version: "1.0"
     ogs_version: "1.0"
     performed_by: ""
-
diff --git a/load_data.py b/load_data.py
index ed5387677e3721ae138b70b60cc59904517a46eb..4f3fbbdad58fe245a2277b8c8a5e2c94d9e03972 100644
--- a/load_data.py
+++ b/load_data.py
@@ -1,4 +1,6 @@
-#!/usr/bin/env python3
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+
 
 import bioblend
 import bioblend.galaxy.objects
@@ -6,21 +8,22 @@ from bioblend import galaxy
 import logging
 import sys
 import deploy_stacks
+import create_input_instance
 
 
 """
 load_data.py
 
-Load data in a galaxy container.
+Find source data files using the information provided in the input file.
+Copy these source data files over into the src_data directory
 
+Load the data into Galaxy using the script provided by Anthony Bretaudeau (setup_data_libraries)
+Also create/update the species history (TODO: Updating history)
 
 
 """
 
 
-class LoadData:
-    def __init__(self, autoload_instance):
-        self.instance = None
 
 
 
diff --git a/run_workflow.py b/run_workflow.py
new file mode 100644
index 0000000000000000000000000000000000000000..836e3e88982589c26a669cd7248b9997bfa67f9a
--- /dev/null
+++ b/run_workflow.py
@@ -0,0 +1,2 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
diff --git a/templates/stack-organism.yml b/templates/stack-organism.yml
index b836476c1ccf295ff017e94567ad9765a4885a75..519b96f55d309b748c52b0b33d231727dce72870 100644
--- a/templates/stack-organism.yml
+++ b/templates/stack-organism.yml
@@ -126,6 +126,8 @@ services:
             GALAXY_CONFIG_ALLOW_LIBRARY_PATH_PASTE: "True"
             GALAXY_CONFIG_USE_REMOTE_USER: "True"
             GALAXY_CONFIG_REMOTE_USER_MAILDOMAIN: "sb-roscoff.fr"
+            GALAXY_DEFAULT_ADMIN_EMAIL: "gga@sb-roscoff.fr"
+            GALAXY_DEFAULT_ADMIN_USER: "gga"
             GALAXY_DEFAULT_ADMIN_PASSWORD: "password"
             GALAXY_CONFIG_ADMIN_USERS: "admin@galaxy.org, gga@sb-roscoff.fr, lgueguen@sb-roscoff.fr, alebars@sb-roscoff.fr"   # admin@galaxy.org is the default (leave it), gogepp@bipaa is a shared ldap user we use to connect
             GALAXY_CONFIG_MASTER_API_KEY: "dev"
diff --git a/undaria_pinnatifida/ADD_ORGA_ADD_GENOME_ADD_OGS.ga b/undaria_pinnatifida/ADD_ORGA_ADD_GENOME_ADD_OGS.ga
deleted file mode 100644
index 05681d1248ef47dc2ea9c001c10742e8e08651a8..0000000000000000000000000000000000000000
--- a/undaria_pinnatifida/ADD_ORGA_ADD_GENOME_ADD_OGS.ga
+++ /dev/null
@@ -1 +0,0 @@
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{"name": "program", "description": "runtime parameter for tool Chado analysis add"}, {"name": "algorithm", "description": "runtime parameter for tool Chado analysis add"}, {"name": "date_executed", "description": "runtime parameter for tool Chado analysis add"}, {"name": "description", "description": "runtime parameter for tool Chado analysis add"}], "position": {"top": 253, "left": 543}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_analysis_add_analysis/analysis_add_analysis/2.3.2", "type": "tool"}}, "annotation": "", "a_galaxy_workflow": "true"}
\ No newline at end of file
diff --git a/undaria_pinnatifida/Galaxy-Workflow-Workflow_constructed_from_history__Ectocarpus_species5_.ga b/undaria_pinnatifida/Galaxy-Workflow-Workflow_constructed_from_history__Ectocarpus_species5_.ga
deleted file mode 100644
index 5573d225085eceabf90ca93ebf79640def88eef3..0000000000000000000000000000000000000000
--- a/undaria_pinnatifida/Galaxy-Workflow-Workflow_constructed_from_history__Ectocarpus_species5_.ga
+++ /dev/null
@@ -1,37 +0,0 @@
-{"uuid": "b5bfbe32-ff35-4b75-a92b-559c78c93d22", "tags": [], "format-version": "0.1", "name": "$WORKFLOWNAME", "version": 0, "steps": {
-
-"0": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{\"name\": \"$OGS$OGSVERSION"}", "id": 0, "uuid": "e9bbfd5b-a5dd-425b-b256-9cabbd9a177c", "errors": null, "name": "Input dataset", "label": null, "inputs": [{"name": "$OGS$VERSION.gff", "description": ""}], "position": {"top": 10, "left": 10}, "annotation": "", "content_id": null, "type": "data_input"},
-
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-
-"2": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{\"name\": \"v$VERSION.fasta\"}", "id": 2, "uuid": "04aec4d2-c320-4988-aa8b-412aff79b62e", "errors": null, "name": "Input dataset", "label": null, "inputs": [{"name": "v$VERSION.fasta", "description": ""}], "position": {"top": 250, "left": 10}, "annotation": "", "content_id": null, "type": "data_input"},
-
-"3": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{\"name\": \"$OGS$VERSION_$DATE.gff\"}", "id": 3, "uuid": "a97eba53-a21d-4055-988e-18bdaa221d23", "errors": null, "name": "Input dataset", "label": null, "inputs": [{"name": "$OGS$VERSION_$DATE.gff", "description": ""}], "position": {"top": 370, "left": 10}, "annotation": "", "content_id": null, "type": "data_input"},
-
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-
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index d0d8ac6f16f1fb93714ad77e42f4cd7b0584d7f9..0000000000000000000000000000000000000000
--- a/undaria_pinnatifida/Galaxy-Workflow-test.ga
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deleted file mode 100644
index e9e1bd31f112f0321356c50c89b2333598e01e71..0000000000000000000000000000000000000000
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