From f8afae335633d63b2d9d20ed59ac60cf3e32ad80 Mon Sep 17 00:00:00 2001 From: John SJ Anderson Date: Mon, 5 Aug 2024 16:25:49 -0700 Subject: [PATCH] Fix broken links [nextstrain/docs.nextstrain.org#14] * Link to "community page on site" rather than "community section on front page" * Update colorbrewer link to HTTPS * Update link to Zika reference GenBank file to current location in repo * Update link to example that was removed from the repo to point to last version before deletion --- docs/examples/examples.rst | 2 +- docs/faq/colors.md | 2 +- docs/faq/import-beast.md | 6 +++++- docs/faq/translate_ref.md | 4 ++-- 4 files changed, 9 insertions(+), 5 deletions(-) diff --git a/docs/examples/examples.rst b/docs/examples/examples.rst index d7b846615..97c3d81ad 100644 --- a/docs/examples/examples.rst +++ b/docs/examples/examples.rst @@ -45,4 +45,4 @@ Nextstrain community ==================== Nextstrain also provides access to analyses by independent groups `stored and accessed via public GitHub repos `__, all of which currently use augur. -For the most up-to-date listing of these please see the `community section on the nextstrain front page. `__ +For the most up-to-date listing of these please see the `community section on the nextstrain site. `__ diff --git a/docs/faq/colors.md b/docs/faq/colors.md index a6b7ab08e..28487ffea 100644 --- a/docs/faq/colors.md +++ b/docs/faq/colors.md @@ -20,7 +20,7 @@ country american samoa #3F50CC country fiji #3F5ED0 ``` -The hexadecimal notation starts with a #, followed by two letters coding for red, green, blue values. If you need advice or inspiration for colors, have a look at [colorbrewer](http://colorbrewer2.org/#type=sequential&scheme=BuGn&n=3). +The hexadecimal notation starts with a #, followed by two letters coding for red, green, blue values. If you need advice or inspiration for colors, have a look at [colorbrewer](https://colorbrewer2.org/#type=sequential&scheme=BuGn&n=3). Pay particular not to mix tabs and spaces for column separation. The line ``` diff --git a/docs/faq/import-beast.md b/docs/faq/import-beast.md index 9d07ea4ac..fabf0a999 100644 --- a/docs/faq/import-beast.md +++ b/docs/faq/import-beast.md @@ -66,4 +66,8 @@ augur import beast --mcc data/beast.mcc.nex --output-tree results/mers.new --most-recent-tip-date 2018.43 ``` -A full [example build can be found here](https://github.com/nextstrain/augur/tree/master/tests/builds/beast_mers). +A full [example build can be found here][]. (N.b., this build has been +removed from the current version of the repository; the link here is +to the last version prior to its removal.) + +[example build can be found here]: https://github.com/nextstrain/augur/blob/73b8a71103bae3a36b49acdee7c7c75a7e69a751/tests/builds/beast_mers/Snakefile diff --git a/docs/faq/translate_ref.md b/docs/faq/translate_ref.md index 2987b3d69..b9cf36996 100644 --- a/docs/faq/translate_ref.md +++ b/docs/faq/translate_ref.md @@ -30,7 +30,7 @@ Augur will only translate genes which have 'CDS' as the feature name, and have a /gene="ENV" ``` -Compare the [original Zika reference on Genbank](https://www.ncbi.nlm.nih.gov/nuccore/KX369547) to the [one used on Nextstrain](https://github.com/nextstrain/zika/blob/master/config/zika_reference.gb). Notice that the genes are designated by `CDS` instead of `mat_peptide` and have an entry for `/gene=` as well as `/product=`. +Compare the [original Zika reference on Genbank](https://www.ncbi.nlm.nih.gov/nuccore/KX369547) to the [one used on Nextstrain](https://github.com/nextstrain/zika/blob/-/phylogenetic/defaults/zika_reference.gb). Notice that the genes are designated by `CDS` instead of `mat_peptide` and have an entry for `/gene=` as well as `/product=`. ### VCF @@ -38,4 +38,4 @@ 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.