import non-API augur docs #9

nextstrain · Sep 25, 2020 · 50fdcbb · 50fdcbb
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diff --git a/src/guides/bioinformatics/index.rst b/src/guides/bioinformatics/index.rst
@@ -11,3 +11,12 @@ How-to guides for performing bioinformatic anaylses with Nextstrain.
    :caption: Table of contents
 
    defining-clades
+   ../../augur/docs/faq/augur_snakemake
+   ../../augur/docs/faq/translate_ref
+   ../../augur/docs/faq/import-beast
+   ../../augur/docs/faq/colors
+   ../../augur/docs/faq/lat_longs
+   ../../augur/docs/faq/vcf_input
+   ../../augur/docs/faq/fasta_input
+   ../../augur/docs/faq/seq_traits
+   ../../augur/docs/examples/examples
diff --git a/src/guides/install/index.rst b/src/guides/install/index.rst
@@ -13,3 +13,4 @@ How-to guides for installing the various Nextstrain tools.
    local-installation
    local-vs-container-install
    windows-help
+   ../../augur/docs/installation/installation
diff --git a/src/guides/share/index.rst b/src/guides/share/index.rst
@@ -14,3 +14,4 @@ How-to guides for visualizing and sharing Nextstrain analyses.
    Download data <download-data>
    nextstrain-groups
    sharing-data
+   ../../augur/docs/faq/community_hosting
diff --git a/src/reference/augur/index.rst b/src/reference/augur/index.rst
@@ -10,5 +10,19 @@ Augur splash page placeholder.
    :titlesonly:
    :caption: Table of contents
 
-   what-is-a-build
+   ../../augur/docs/index
    introduction-to-augur
+   what-is-a-build
+   ../../augur/docs/usage/usage
+   ../../augur/docs/usage/json_format
+   ../../augur/docs/usage/envvars
+   ../../augur/docs/releases/releases
+   ../../augur/docs/releases/changelog
+   ../../augur/docs/releases/v6
+   ../../augur/docs/releases/migrating-v5-v6
+   ../../augur/docs/releases/breaking
+   ../../augur/docs/releases/auspice-compatibility
+   ../../augur/docs/faq/metadata
+   ../../augur/docs/faq/clades
+   ../../augur/docs/faq/refine
+   ../../augur/docs/authors/authors
diff --git a/src/tutorials/index.rst b/src/tutorials/index.rst
@@ -13,3 +13,5 @@ Tutorials to help you get started with Nextstrain!
    quickstart
    SARS-CoV-2/index
    zika
+   ../augur/docs/tutorials/zika_tutorial
+   ../augur/docs/tutorials/tb_tutorial