What it does

1. The tool asks the admin to enter a species_name and automatically download the last release of the corresponding gtf annotation file on Ensembl.

2. The tool calls ALFA.py to generate the alfa indexes from this gtf file.

3. Resulting indexes are stored in the child directory alfa_indexes/ of the dir <galaxy_data_manager_data_path> defined in config/galaxy.ini

4. Finally, the tool adds the new entry to the table alfa_indexes.loc. This .loc file is where the data table alfa_indexes points, as defined in config/shed_tool_data_table.conf.xml

5. At the end of the process, when a user will use alfa , the built-in indexes corresponding to the species_name will be available