From 50fdcbb4b43e931c5641a90ffcac12bd3f36cbb8 Mon Sep 17 00:00:00 2001 From: eharkins Date: Fri, 25 Sep 2020 16:55:42 -0400 Subject: [PATCH] import non-API augur docs #9 --- src/guides/bioinformatics/index.rst | 9 +++++++++ src/guides/install/index.rst | 1 + src/guides/share/index.rst | 1 + src/reference/augur/index.rst | 16 +++++++++++++++- src/tutorials/index.rst | 2 ++ 5 files changed, 28 insertions(+), 1 deletion(-) diff --git a/src/guides/bioinformatics/index.rst b/src/guides/bioinformatics/index.rst index b8a07ec2..27e71af8 100644 --- 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 index 2766b007..39bf32ef 100644 --- 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 index 12223b47..7aa82bf7 100644 --- 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 nextstrain-groups sharing-data + ../../augur/docs/faq/community_hosting diff --git a/src/reference/augur/index.rst b/src/reference/augur/index.rst index 6af86e23..8f5bb113 100644 --- 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 index 1f61f8ed..9a5e32fe 100644 --- 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