... | ... | @@ -8,6 +8,57 @@ In this section, you will find a list of homemade commands available through `ma |
|
|
|
|
|
*The following list might not correspond exactly to the scripts available. We recommend to go through the help section of the `manage.py` command.*
|
|
|
|
|
|
To run a script, in the backend docker container or in a custom python env:
|
|
|
|
|
|
```
|
|
|
manage.py your_script
|
|
|
manage.py help your_script # Display instructions
|
|
|
```
|
|
|
|
|
|
### Pre-build scripts from Django
|
|
|
|
|
|
For all scripts from Django, Please refer to the [original documentation](https://docs.djangoproject.com/en/3.1/ref/django-admin/).
|
|
|
|
|
|
### Custom scripts
|
|
|
|
|
|
#### Test DB
|
|
|
|
|
|
* create_light_db
|
|
|
|
|
|
#### Populate the database
|
|
|
|
|
|
##### Import annotations
|
|
|
|
|
|
###### KEGG
|
|
|
|
|
|
* create_update_kegg_ko
|
|
|
|
|
|
###### EggNOG
|
|
|
|
|
|
* create_update_eggnog
|
|
|
* create_eggnog_functional_cat
|
|
|
|
|
|
###### Taxonomy
|
|
|
|
|
|
* build_hierarchy
|
|
|
|
|
|
##### Import genes
|
|
|
|
|
|
###### General rules
|
|
|
|
|
|
###### IGC
|
|
|
|
|
|
* import_igc_annotation
|
|
|
* import_igc_sequences
|
|
|
|
|
|
###### Virgo
|
|
|
|
|
|
* import_virgo_eggnog
|
|
|
* import_virgo_genes
|
|
|
* import_virgo_kegg
|
|
|
* import_virgo_sequences
|
|
|
* import_virgo_taxonomy
|
|
|
|
|
|
#### Pre computed metrics
|
|
|
|
|
|
* compute_stats |