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

@@ -141,7 +141,7 @@ class LoadData(speciesData.SpeciesData):
 
             for fname, files in folders.items():
                 if fname and files:
-                    folder_name = fname[len(data_dir_root) + 1:]
+                    folder_name = fname[len(CONTAINER_DATA_DIR_ROOT) + 1:]
                     logging.info("Creating folder: %s" % folder_name)
                     folder = self.create_deep_folder(prj_lib, folder_name)
 
@@ -183,11 +183,9 @@ class LoadData(speciesData.SpeciesData):
                             logging.info("Skipping useless file '%s'" % single_file)
                             continue
 
-                        single_file_path=os.path.join(CONTAINER_DATA_DIR_ROOT,single_file)
-
                         logging.info("Adding file '%s' with type '%s' and name '%s'" % (single_file, ftype, clean_name))
                         datasets = prj_lib.upload_from_galaxy_fs(
-                            single_file_path,
+                            single_file,
                             folder=folder,
                             link_data_only='link_to_files',
                             file_type=ftype,