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

 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
+import re
 
 import bioblend
 import argparse
@@ -141,7 +142,7 @@ class LoadData(speciesData.SpeciesData):
 
             for fname, files in folders.items():
                 if fname and files:
-                    folder_name = fname[len(CONTAINER_DATA_DIR_ROOT) + 1:]
+                    folder_name = re.sub(data_dir_root, CONTAINER_DATA_DIR_ROOT, fname)
                     logging.info("Creating folder: %s" % folder_name)
                     folder = self.create_deep_folder(prj_lib, folder_name)
 
@@ -183,7 +184,8 @@ class LoadData(speciesData.SpeciesData):
                             logging.info("Skipping useless file '%s'" % single_file)
                             continue
 
-                        single_file_path_in_container=os.path.join(CONTAINER_DATA_DIR_ROOT, single_file)
+                        single_file_relative_path = re.sub(data_dir_root, CONTAINER_DATA_DIR_ROOT, single_file)
+                        single_file_path_in_container=os.path.join(CONTAINER_DATA_DIR_ROOT, single_file_relative_path)
 
                         logging.info("Adding file '%s' with type '%s' and name '%s'" % (single_file_path_in_container, ftype, clean_name))
                         datasets = prj_lib.upload_from_galaxy_fs(