bactopia-atb-downloader
Download All-the-Bacteria assemblies based on input query
Usage
bactopia-atb-downloader [OPTIONS]
Required Options
| Option | Type | Default | Description |
|---|---|---|---|
--query, -q | STRING | The species name, taxid, accession to query and download |
ATB Download Options
| Option | Type | Default | Description |
|---|---|---|---|
--outdir, -o | STRING | ./atb-assemblies | Directory to download ATB assemblies to |
--atb-file-list-url, -a | STRING | https://osf.io/download/4yv85/ | The URL to the ATB file list |
--dry-run, -d | BOOL | false | Do not download any files, just show what would be downloaded |
--progress, -p | BOOL | false | Show download progress bar |
--cpus | INT | 4 | The total number of cpus to use for downloading and compressing |
--uncompressed, -u | BOOL | false | Do not compress the downloaded files |
--remove-archives, -r | BOOL | false | Remove the downloaded tar.xz archives after extracting samples |
NCBI API Options
| Option | Type | Default | Description |
|---|---|---|---|
--ncbi-api-key, -k | STRING | The API key to use for the NCBI API | |
--chunk-size, -c | INT | 200 | The size of the chunks to split the list into |
Additional Options
| Option | Type | Default | Description |
|---|---|---|---|
--force | BOOL | false | Overwrite existing files |
--verbose | BOOL | false | Print debug related text |
--silent | BOOL | false | Only critical errors will be printed |
--version, -V | BOOL | false | Show the version and exit. |