bactopia-pubmlst-build
Build PubMLST databases for use with the 'mlst' Bactopia Tool.
Usage
bactopia-pubmlst-build [OPTIONS]
Required Options
| Option | Type | Default | Description |
|---|---|---|---|
--database, -d | STRING | A known organism database to download. (Use 'all' to download all databases.) |
Build Options
| Option | Type | Default | Description |
|---|---|---|---|
--ignore | STRING | afumigatus,blastocystis,calbicans,cbotulinum,cglabrata,ckrusei,ctropicalis,csinensis,kseptempunctata,rmlst,sparasitica,test,tpallidum,tvaginalis | A comma separated list of databases to ignore |
--skip-download | BOOL | false | Skip downloading the database files |
--skip-blast | BOOL | false | Skip building the BLAST database |
--force | BOOL | false | Force overwrite of existing files |
API Options
| Option | Type | Default | Description |
|---|---|---|---|
--site, -s | CHOICE (pubmlst, pasteur) | pubmlst | Only print citation matching a given name |
--token-dir, -t | STRING | /home/rpetit3/.bactopia | The directory where the token file is saved |
--out-dir, -o | STRING | ./bactopia-mlst | The directory where the database files will be saved |
Additional Options
| Option | Type | Default | Description |
|---|---|---|---|
--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. |