docs: Update installation and AWS Batch pages to account for new Cond…

…a runner

doc/aws-batch.md

@@ -18,9 +18,9 @@ This uploads the [`zika-tutorial/` directory][] to S3, submits the
 Batch job, monitors the job status, streams the job logs to your terminal, and
 downloads build results back to the `zika-tutorial/` directory.
 
-The interface aims to be very similar to that of local builds (either
-containerized with Docker or native), so the `nextstrain build` command stays
-in the foreground and result files are written back directly to the local build
+The interface aims to be very similar to that of local builds (run in the
+Docker, Conda, or native runtimes), so the `nextstrain build` command stays in
+the foreground and result files are written back directly to the local build
 directory.  Alternatively, you can specify the `--detach` option to run AWS
 Batch builds in the background once they're submitted.  The Nextstrain CLI will
 tell you how to reattach to the build later to view the logs and download the

doc/installation.md

@@ -70,8 +70,8 @@ build` and `nextstrain view`.
 The default runner is Docker, using the [nextstrain/base][] container image.
 Containers provide a tremendous amount of benefit for scientific workflows by
 isolating dependencies and increasing reproducibility.  However, they're not
-always appropriate, so a "native" runner is also supported.  The installation
-and setup of supported runners is described below.
+always appropriate, so a Conda runner and "native" runner are also supported.
+The installation and setup of supported runners is described below.
 
 [nextstrain/base]: https://github.com/nextstrain/docker-base
 
@@ -97,18 +97,32 @@ setup](#checking-your-setup).
 [windows issue]: https://github.com/nextstrain/cli/issues/31
 [WSL2]: https://docs.microsoft.com/en-us/windows/wsl/wsl2-index
 
+### Conda
+
+[Conda][] is a very popular packaging system freely-available for all
+platforms.  When you use Nextstrain CLI's built-in Conda support, you don't
+need to install any other Nextstrain software dependencies yourself as they're
+automatically managed in an isolated location (isolated even from other Conda
+environments you may manage yourself).
+
+On macOS and Linux, run `nextstrain setup conda` to get started.
+
+This runner is not directly supported on Windows, but you can use [WSL2][] to
+"switch" to Linux and run the above setup command.
+
 ### Native
 
-The "native" runner allows you to use the Nextstrain CLI without installing
-Docker, for cases when you cannot or do not want to use containers.
+The "native" runner allows you to use the Nextstrain CLI with your own ambient
+setup, for when you cannot or do not want to have Nextstrain CLI manage its own
+environment.
 
 However, you will need to make sure all of the Nextstrain software dependencies
-are available locally or "natively" on your computer.  The easiest and most
-common way to do this is by using [Conda][] to install our [Conda
-environment](https://github.com/nextstrain/conda#readme), as [documented
-here](https://nextstrain.org/docs/getting-started/local-installation).  It is
-also possible to install the required Nextstrain software [Augur][] and
-[Auspice][] and their dependencies manually, although this is not recommended.
+are available locally or "natively" on your computer.  A common way to do this
+is by manually using [Conda][] to manage your own environment that includes the
+required software, however you're responsible for making sure the correct
+software is installed and kept up-to-date.  It is also possible to install the
+required Nextstrain software [Augur][] and [Auspice][] and their dependencies
+manually, although this is not recommended.
 
 Once you've installed dependencies, proceed with [checking your
 setup](#checking-your-setup).
@@ -144,28 +158,35 @@ based on what's available.  You should see output similar to the following:
     ✔ yes: containers have access to >2 GiB of memory
     ✔ yes: image is new enough for this CLI version
 
+    # conda is supported
+    ✔ yes: operating system is supported
+    ✔ yes: runtime data dir doesn't have spaces
+    ✔ yes: snakemake is installed and runnable
+    ✔ yes: augur is installed and runnable
+    ✔ yes: auspice is installed and runnable
+
     # native is not supported
-    ✔ yes: snakemake is installed
-    ✘ no: augur is installed
-    ✘ no: auspice is installed
+    ✔ yes: snakemake is installed and runnable
+    ✘ no: augur is installed and runnable
+    ✘ no: auspice is installed and runnable
 
     # aws-batch is not supported
     ✘ no: job description "nextstrain-job" exists
     ✘ no: job queue "nextstrain-job-queue" exists
     ✘ no: S3 bucket "nextstrain-jobs" exists
 
-    All good!  Supported Nextstrain environments: docker
+    All good!  Supported Nextstrain environments: docker, conda
 
     Setting default environment to docker.
 
 If the output doesn't say "All good!" and list at least one supported
-Nextstrain computing environment (typically Docker or native), then something
-may be wrong with your installation.
+Nextstrain computing environment (typically Docker, Conda, or native), then
+something may be wrong with your installation.
 
 The default is written to the _~/.nextstrain/config_ file.  If multiple
 environments are supported, you can override the default for specific runs
-using command-line options such as `--docker`, `--native`, and `--aws-batch`,
-e.g. `nextstrain build --native …`.
+using command-line options such as `--docker`, `--conda`, `--native`, and
+`--aws-batch`, e.g. `nextstrain build --native …`.
 
 
 [Augur]: https://github.com/nextstrain/augur