Release 2.0

gga_load_data.py:

• Factorize goto_species_dir(), create_galaxy_instance(), run_tool(), get_species_dir()
• Move constants at the beginning
• Revert upload_from_local() to upload_from_galaxy_fs() (to enable symlink, instead of copy)
• Add missing get_bam_label()

README:

• update contributors

gga_load_data.py

@@ -10,7 +10,7 @@ import time
 import json
 import yaml
 
-from bioblend.galaxy.objects import GalaxyInstance
+from bioblend import galaxy
 
 import utilities
 import speciesData
@@ -275,7 +275,7 @@ class LoadData(speciesData.SpeciesData):
         """
 
         logging.info("Connecting to the galaxy instance (%s)" % self.instance_url)
-        self.instance = GalaxyInstance(url=self.instance_url,
+        self.instance = galaxy.GalaxyInstance(url=self.instance_url,
                                               email=self.config["galaxy_default_admin_email"],
                                               password=self.config["galaxy_default_admin_password"]
                                               )