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

@@ -101,7 +101,7 @@ class LoadData(speciesData.SpeciesData):
 
         return histories
 
-    def setup_library(self, instance, data_dir_root='./src_data'):
+    def setup_library(self, data_dir_root='./src_data'):
         """
         Create a "Project Data" library in galaxy, mirroring the "src_data" folder of the current organism
         directory tree
@@ -111,7 +111,7 @@ class LoadData(speciesData.SpeciesData):
 
         self.goto_species_dir()
 
-        gio = GalaxyInstance(url=self.instance_url,
+        instance = GalaxyInstance(url=self.instance_url,
                                               email=self.config["galaxy_default_admin_email"],
                                               password=self.config["galaxy_default_admin_password"]
                                               )
@@ -372,7 +372,7 @@ if __name__ == "__main__":
 
             # Load the datasets into a galaxy library
             logging.info("Setting up library for {0} {1}".format(load_data_for_current_species.genus, load_data_for_current_species.species))
-            load_data_for_current_species.setup_library(load_data_for_current_species.instance)
+            load_data_for_current_species.setup_library()
             logging.debug("Successfully set up library in galaxy for {0} {1}".format(load_data_for_current_species.genus, load_data_for_current_species.species))
 
             # Set or get the history for the current organism