.. default-role:: literal .. role:: command-reference(ref) .. program:: nextstrain view .. _nextstrain view: =============== nextstrain view =============== .. code-block:: none usage: nextstrain view [options] nextstrain view --help Visualizes a completed pathogen builds or narratives in Auspice, the Nextstrain visualization app. :option:`` may be a `dataset (.json) file`_ or `narrative (.md) file`_ to start Auspice and directly open the specified dataset or narrative in a browser. Adjacent datasets and/or narratives may also be viewable as an appropriate data directory for Auspice is automatically inferred from the file path. :option:`` may also be a directory with one of the following layouts:: / ├── auspice/ │ └── *.json └── narratives/ └── *.md / ├── auspice/ │ └── *.json └── *.md / ├── *.json └── narratives/ └── *.md / ├── *.json └── *.md Dataset and narrative files will be served, respectively, from **auspice** and/or **narratives** subdirectories under the given :option:`` if the subdirectories exist. Otherwise, files will be served from the given directory :option:`` itself. If your pathogen build directory follows our conventional layout by containing an **auspice** directory (and optionally a **narratives** directory), then you can give `nextstrain view` the same path as you do `nextstrain build`. Note that by convention files named **README.md** or **group-overview.md** will be ignored for the purposes of finding available narratives. .. _dataset (.json) file: https://docs.nextstrain.org/page/reference/glossary.html#term-dataset .. _narrative (.md) file: https://docs.nextstrain.org/page/reference/glossary.html#term-narrative positional arguments ==================== .. option:: Path to a directory containing dataset JSON and/or narrative Markdown files for Auspice, or a directory containing an auspice/ and/or narratives/ directory, or a specific dataset JSON or narrative Markdown file. options ======= .. option:: --help, -h Show a brief help message of common options and exit .. option:: --help-all Show a full help message of all options and exit .. option:: --open Open a web browser automatically (the default) .. option:: --no-open Do not open a web browser automatically .. option:: --allow-remote-access Allow other computers on the network to access the website (alias for --host=0.0.0.0) .. option:: --host Listen on the given hostname or IP address instead of the default 127.0.0.1. You may also set the :envvar:`HOST` environment variable to change the default. .. option:: --port Listen on the given port instead of the default port 4000. You may also set the :envvar:`PORT` environment variable to change the default. runtime selection options ========================= Select the Nextstrain runtime to use, if the default is not suitable. .. option:: --docker Run commands inside a container image using Docker. (default) .. option:: --ambient Run commands in the ambient environment, outside of any container image or managed environment. .. option:: --conda Run commands with access to a fully-managed Conda environment. .. option:: --singularity Run commands inside a container image using Singularity. runtime options =============== Options shared by all runtimes. .. option:: --env [=] Set the environment variable ```` to the value in the current environment (i.e. pass it thru) or to the given ````. May be specified more than once. Overrides any variables of the same name set via :option:`--envdir`. When this option or :option:`--envdir` is given, the default behaviour of automatically passing thru several "well-known" variables is disabled. The "well-known" variables are ``AUGUR_RECURSION_LIMIT``, ``AUGUR_MINIFY_JSON``, ``AWS_ACCESS_KEY_ID``, ``AWS_SECRET_ACCESS_KEY``, ``AWS_SESSION_TOKEN``, ``ID3C_URL``, ``ID3C_USERNAME``, ``ID3C_PASSWORD``, ``RETHINK_HOST``, and ``RETHINK_AUTH_KEY``. Pass those variables explicitly via :option:`--env` or :option:`--envdir` if you need them in combination with other variables. .. option:: --envdir Set environment variables from the envdir at ````. May be specified more than once. An envdir is a directory containing files describing environment variables. Each filename is used as the variable name. The first line of the contents of each file is used as the variable value. When this option or :option:`--env` is given, the default behaviour of automatically passing thru several "well-known" variables is disabled. Envdirs may also be specified by setting ``NEXTSTRAIN_RUNTIME_ENVDIRS`` in the environment to a ``:``-separated list of paths. See the description of :option:`--env` for more details. development options =================== These should generally be unnecessary unless you're developing Nextstrain. .. option:: --image Container image name to use for the Nextstrain runtime (default: nextstrain/base for Docker and AWS Batch, docker://nextstrain/base for Singularity) .. option:: --augur Replace the image's copy of augur with a local copy .. option:: --auspice Replace the image's copy of auspice with a local copy .. option:: --fauna Replace the image's copy of fauna with a local copy .. option:: --exec Program to run inside the runtime development options for --docker ================================ .. option:: --docker-arg ... Additional arguments to pass to `docker run` In some contexts, it may be preferable to provide environment variables instead of command-line options: .. envvar:: HOST Hostname or IP address on which to listen by default. Ignored if :option:`--host` or :option:`--allow-remote-access` is provided. .. envvar:: PORT Port on which to listen by default. Ignored if :option:`--port` is provided.