| 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 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 (https://toolshed.g2.bx.psu.edu/view/charles-bernard/alfa), the built-in indexes corresponding to the 'species_name' will be available |
| Name | Version | Type | |
|---|---|---|---|
| bedtools | 2.24 | package | |
| matplotlib | 1.4 | package | |
| samtools | 1.2 | package | |
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| build ALFA indexes from automatically downloaded gtf annotation file | 0.0.1 | 16.01 | |
| Name | Version | Data Tables |
|---|---|---|
| build_alfa_indexes | 0.0.1 | alfa_indexes |