bactopia-download
Builds Bactopia environments for use with Nextflow.
Usage
bactopia-download UNKNOWN [OPTIONS]
Arguments
| Argument | Type | Required | Description |
|---|---|---|---|
UNKNOWN | UNPROCESSED | No |
Required Options
| Option | Type | Default | Description |
|---|---|---|---|
--bactopia-path | STRING | Directory where Bactopia repository is stored |
Build Related Options
| Option | Type | Default | Description |
|---|---|---|---|
--envtype | CHOICE (conda, docker, singularity, all) | conda | The type of environment to build |
--wf | STRING | bactopia | Build a environment for a the given workflow |
--build-all | BOOL | false | Builds all environments for Bactopia workflows |
--condadir | STRING | /home/rpetit3/.bactopia/conda | Directory to create Conda environments (NXF_CONDA_CACHEDIR env variable takes precedence) |
--use-conda | BOOL | false | Use Conda for building Conda environments instead of Mamba |
--registry | STRING | quay.io | Registry to pull Docker containers from |
--singularity_cache | STRING | /home/rpetit3/.bactopia/singularity | Directory to download Singularity images (NXF_SINGULARITY_CACHEDIR env variable takes precedence) |
--singularity_pull_docker_container | BOOL | false | Force conversion of Docker containers, instead downloading Singularity images directly |
--force_rebuild | BOOL | false | Force overwrite of existing pre-built environments |
--max_retry | INT | 3 | Maximum times to attempt creating Conda environment. (Default: 3) |
Additional Options
| Option | Type | Default | Description |
|---|---|---|---|
--dry-run | BOOL | false | Show environments that would be built, without building them |
--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. |