|
|
The **init_ncbi_taxdump** module download and decompress the NCBI taxdump archive into the target path. Local taxonomy files can be use by validate (see [Validate Section](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Validate)) and curegen (see the [Curegen section](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Curegen)) modules.
|
|
|
|
|
|
# Inputs
|
|
|
|
|
|
* Folder path where to download and decompress the NCBI taxdump archive
|
|
|
|
|
|
# Command-line Arguments
|
|
|
|
|
|
| complete flag argument | short flag | Default value | Summary |
|
|
|
| --- | --- | --- | --- |
|
|
|
| `--folder_path` | `-f` | current working directory | Folder path where to download and decompress the NCBI taxdump archive |
|
|
|
|
|
|
|
|
|
# Example of commands
|
|
|
|
|
|
This command will download the latest NCBI taxonomy files at the address ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/ and decompress these files into the folder `path/to/local/ncbi_taxo`
|
|
|
|
|
|
```
|
|
|
mkbdr init_ncbi_taxdump --folder_path path/to/local/ncbi_taxo
|
|
|
```
|
|
|
|
|
|
# Outputs
|
|
|
|
|
|
Local NCBI Taxonomy files can be useful if you need to add new custom species to the tree of life and need to edit a local taxonomy.
|
|
|
|
|
|
A thorough description of NCBI taxonomy files is available [here](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Files-definition#ncbi-taxonomies-file)
|
|
|
|
|
|
|
|
|
|
|
|
|