From 3271a58a51ec9a120aaeecaddaafd6b8e9cfd00c Mon Sep 17 00:00:00 2001 From: eharkins Date: Fri, 20 Nov 2020 12:15:27 -0800 Subject: [PATCH] Add warning to docs fetched by docs.nextstrain.org --- docs/contribute/DEV_DOCS.md | 10 ++++++++++ docs/examples/examples.rst | 11 +++++++++++ docs/faq/colors.md | 10 ++++++++++ docs/faq/fasta_input.md | 12 +++++++++++- docs/faq/import-beast.md | 11 +++++++++++ docs/faq/lat_longs.md | 10 ++++++++++ docs/faq/seq_traits.md | 10 ++++++++++ docs/faq/translate_ref.md | 12 +++++++++++- docs/faq/vcf_input.md | 12 +++++++++++- docs/installation/installation.md | 10 ++++++++++ docs/tutorials/tb_tutorial.md | 10 ++++++++++ docs/tutorials/zika_tutorial.md | 10 ++++++++++ docs/usage/augur_snakemake.md | 10 ++++++++++ 13 files changed, 135 insertions(+), 3 deletions(-) diff --git a/docs/contribute/DEV_DOCS.md b/docs/contribute/DEV_DOCS.md index 77f83edf5..e02c6c449 100644 --- a/docs/contribute/DEV_DOCS.md +++ b/docs/contribute/DEV_DOCS.md @@ -1,4 +1,14 @@ # Augur Development Docs for Contributors + + + + + + + + + + Thank you for helping us to improve Augur! This document describes: diff --git a/docs/examples/examples.rst b/docs/examples/examples.rst index d7b846615..c0387d085 100644 --- a/docs/examples/examples.rst +++ b/docs/examples/examples.rst @@ -1,6 +1,17 @@ ============================= Examples of Augur in the wild ============================= +.. + WARNING + Do not edit this file from within the docs.nextstrain.org repository. + It is fetched from another repository to be included in the docs.nextstrain.org build. + So, if you edit it after it is fetched into docs.nextstrain.org, your changes will be lost. + Instead, edit this file in its own repository and commit your changes there. + For more details on this (temporary) implementation, see https://github.com/nextstrain/docs.nextstrain.org#fetching-of-documents-from-other-repositories + This file is fetched from: https://github.com/nextstrain/augur/blob/master/docs/examples/examples.rst + WARNING + WARNING + WARNING We really enjoy hearing about people using Augur. If you use Augur to do your work, we'd love to add it to this page! Let us know about it by `opening an diff --git a/docs/faq/colors.md b/docs/faq/colors.md index a6b7ab08e..48777bc04 100644 --- a/docs/faq/colors.md +++ b/docs/faq/colors.md @@ -1,4 +1,14 @@ # Adding Custom Trait Colors + + + + + + + + + + Auspice uses a number of default color schemes to color the tree using meta data or values that the augur pipeline computed. In some cases these defaults are not suitable for particular type of data, and you'd like to use your own color schemes. diff --git a/docs/faq/fasta_input.md b/docs/faq/fasta_input.md index 737e9f3e1..2afa08d80 100644 --- a/docs/faq/fasta_input.md +++ b/docs/faq/fasta_input.md @@ -1,4 +1,14 @@ # Using Fasta Input + + + + + + + + + + If you would like to run augur on viral data, or bacterial SNP data, you probably would like to start with Fasta sequence data. @@ -8,4 +18,4 @@ Your sequence data should * consist of homologous sequences that can be aligned unambiguously * needs to contain sufficient diversity to allow reliable tree reconstruction -* should be of similar length. Mixing short sequences (300bp) with much longer ones (10000bp) often yields unexpected results. \ No newline at end of file +* should be of similar length. Mixing short sequences (300bp) with much longer ones (10000bp) often yields unexpected results. diff --git a/docs/faq/import-beast.md b/docs/faq/import-beast.md index 489b2ae5b..01e25a55d 100644 --- a/docs/faq/import-beast.md +++ b/docs/faq/import-beast.md @@ -1,4 +1,15 @@ ## Importing BEAST MCC trees into augur + + + + + + + + + + + This documentation details how to import BEAST MCC trees using `augur import beast`. Currently this is most useful for producing auspice-compatable output using `augur export`, however in the future we will provide instructions on how to perform additional analysis using other augur tools. diff --git a/docs/faq/lat_longs.md b/docs/faq/lat_longs.md index e19c81d7a..180ebce86 100644 --- a/docs/faq/lat_longs.md +++ b/docs/faq/lat_longs.md @@ -1,4 +1,14 @@ # Adding Custom Lat-Long Data + + + + + + + + + + To place sequences on a map, auspice needs to know where the locations you specify are on the globe. These coordinates are provided by augur and augur has preset coordinates for many places. For example, for `region`, `country`, and some `division`s augur already knows many lat-long coordinates (see which ones it already knows by checking the list [here](https://github.com/nextstrain/augur/blob/master/augur/data/lat_longs.tsv)). diff --git a/docs/faq/seq_traits.md b/docs/faq/seq_traits.md index 3f75fe853..bae8009d0 100644 --- a/docs/faq/seq_traits.md +++ b/docs/faq/seq_traits.md @@ -1,4 +1,14 @@ # Inferring Sequence Traits (like Drug Resistance) + + + + + + + + + + Unfortunately this method currently only works with VCF-input files. It will be updated to work with Fasta-input soon! diff --git a/docs/faq/translate_ref.md b/docs/faq/translate_ref.md index 2987b3d69..083887d5e 100644 --- a/docs/faq/translate_ref.md +++ b/docs/faq/translate_ref.md @@ -1,4 +1,14 @@ # Finding a `translate` and `align` reference file + + + + + + + + + + In order to correctly align and annotate the genes in your sequences, augur uses an annotated reference sequence in 'Genbank' format (if Fasta input) or 'GFF' format (if VCF input). @@ -38,4 +48,4 @@ You can also find an appropriate GFF annotation reference on GenBank. Be sure to To download a file from GenBank, use the 'send to' button in the top-right corner, then select 'Complete Record', 'File', and 'GFF3' for the format. -You will have to modify the first column of the GFF so that it matches the `CHROM` (first column) of your VCF file. \ No newline at end of file +You will have to modify the first column of the GFF so that it matches the `CHROM` (first column) of your VCF file. diff --git a/docs/faq/vcf_input.md b/docs/faq/vcf_input.md index 244325646..e372a0f11 100644 --- a/docs/faq/vcf_input.md +++ b/docs/faq/vcf_input.md @@ -1,4 +1,14 @@ # Using VCF Input + + + + + + + + + + If you would like to run augur on whole-genome bacterial data, you probably would like to start with VCF sequence data. (Note that if you have bacterial SNP data, this may be in Fasta format.) @@ -29,4 +39,4 @@ NC_000962 80194 80623 IG71_Rv0071-Rv0072 _(Optional)_ Bacteria can have thousands of genes, and translating all of them can take quite a bit of time. If you wouldn't like to translate all of them, you can provide a list of genes that you'd like to include in the analysis, and only these will be processed. For example, you might include a list of genes that are associated with drug-resistance. -To do this, simply create a file with a list of the genes you'd like to include, with one gene name per line. You can then pass this to `augur translate`. \ No newline at end of file +To do this, simply create a file with a list of the genes you'd like to include, with one gene name per line. You can then pass this to `augur translate`. diff --git a/docs/installation/installation.md b/docs/installation/installation.md index c963ab713..6a3f9e36b 100644 --- a/docs/installation/installation.md +++ b/docs/installation/installation.md @@ -1,4 +1,14 @@ # Installation + + + + + + + + + + * [Using conda](#using-conda) * [Using pip from PyPi](#using-pip-from-pypi) diff --git a/docs/tutorials/tb_tutorial.md b/docs/tutorials/tb_tutorial.md index c40b2965e..3b8e7e7b7 100644 --- a/docs/tutorials/tb_tutorial.md +++ b/docs/tutorials/tb_tutorial.md @@ -1,4 +1,14 @@ # MTb tutorials using vcf data + + + + + + + + + + This tutorial explains how to create a Nextstrain build for Tuberculosis sequences. However, much of it will be applicable to any run where you are starting with [VCF](https://en.wikipedia.org/wiki/Variant_Call_Format) files rather than [FASTA](https://en.wikipedia.org/wiki/FASTA_format) files. diff --git a/docs/tutorials/zika_tutorial.md b/docs/tutorials/zika_tutorial.md index f7bafb66b..c452795cf 100644 --- a/docs/tutorials/zika_tutorial.md +++ b/docs/tutorials/zika_tutorial.md @@ -1,4 +1,14 @@ # Zika tutorial -- fasta input + + + + + + + + + + The tool-chain [*augur*](https://github.com/nextstrain/augur) is the bioinformatics engine of nextstrain and produces the files that can be visualized in the webbrowser using [*auspice*](https://github.com/nextstrain/auspice). Augur consists of a number of tools that allow the user to filter and align sequences, build trees, and integrate the phylogenetic analysis with meta data. diff --git a/docs/usage/augur_snakemake.md b/docs/usage/augur_snakemake.md index b01fb7d26..ce982a9e4 100644 --- a/docs/usage/augur_snakemake.md +++ b/docs/usage/augur_snakemake.md @@ -1,4 +1,14 @@ ## Augur and snakemake + + + + + + + + + + The output of one augur command serves as input to the next and hence these commands need to be executed in order. This is a common pattern in bioinformatics and multiple tools -- so called workflow managers -- exist to facilitate this.