From 7c0426628299de308c58acbc2da60a61422dfafd Mon Sep 17 00:00:00 2001 From: j23414 Date: Sun, 19 Mar 2023 16:18:14 -0700 Subject: [PATCH 1/5] docs: drop obsolete fauna instructions --- README.md | 25 ++++++++++++++++++------- 1 file changed, 18 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index e8433e5a..8516d443 100644 --- a/README.md +++ b/README.md @@ -5,8 +5,8 @@ This is the [Nextstrain](https://nextstrain.org) build for dengue, visible at The build encompasses fetching data, preparing it for analysis, doing quality control, performing analyses, and saving the results in a format suitable for -visualization (with [auspice][]). This involves running components of -Nextstrain such as [fauna][] and [augur][]. +visualization (with [auspice][]). These steps involves running +[augur][] subcommands. All dengue-specific steps and functionality for the Nextstrain pipeline should be housed in this repository. @@ -42,12 +42,24 @@ specifies its file inputs and output and also its parameters. There is little re rule should be able to be reasoned with on its own. -### fauna / RethinkDB credentials +### GenBank vs Example Dataset -This build starts by pulling sequences from our live [fauna][] database (a RethinkDB instance). This -requires environment variables `RETHINK_HOST` and `RETHINK_AUTH_KEY` to be set. +This build starts by pulling preprocessed sequence and metadata files from: -If you don't have access to our database, you can run the build using the +* https://data.nextstrain.org/files/dengue/sequences_all.fasta.zst +* https://data.nextstrain.org/files/dengue/metadata_all.tsv.zst +* https://data.nextstrain.org/files/dengue/sequences_denv1.fasta.zst +* https://data.nextstrain.org/files/dengue/metadata_denv1.tsv.zst +* https://data.nextstrain.org/files/dengue/sequences_denv2.fasta.zst +* https://data.nextstrain.org/files/dengue/metadata_denv2.tsv.zst +* https://data.nextstrain.org/files/dengue/sequences_denv3.fasta.zst +* https://data.nextstrain.org/files/dengue/metadata_denv3.tsv.zst +* https://data.nextstrain.org/files/dengue/sequences_denv4.fasta.zst +* https://data.nextstrain.org/files/dengue/metadata_denv4.tsv.zst + +The above datasets have been preprocessed and cleaned from GenBank and are updated at regular intervals. + +Alternatively, you can run the build using the example data provided in this repository. Before running the build, copy the example sequences into the `data/` directory like so: @@ -61,7 +73,6 @@ With access to AWS, this can be more quickly run as: nextstrain build --aws-batch --aws-batch-cpus 4 --aws-batch-memory 7200 . --jobs 4 [Nextstrain]: https://nextstrain.org -[fauna]: https://github.com/nextstrain/fauna [augur]: https://github.com/nextstrain/augur [auspice]: https://github.com/nextstrain/auspice [snakemake cli]: https://snakemake.readthedocs.io/en/stable/executable.html#all-options From fc3007fb682998e0a7490ff6fe7c43dfa1941a25 Mon Sep 17 00:00:00 2001 From: j23414 Date: Sun, 19 Mar 2023 16:45:05 -0700 Subject: [PATCH 2/5] docs: update nextstrain install links and instructions --- README.md | 20 +++++++++----------- 1 file changed, 9 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index 8516d443..25d5ea22 100644 --- a/README.md +++ b/README.md @@ -15,18 +15,18 @@ housed in this repository. ## Usage +See the [Installing Nextstrain guide][] for how to install the `nextstrain` command. + If you're unfamiliar with Nextstrain builds, you may want to follow our -[quickstart guide][] first and then come back here. +[Running a Pathogen Workflow guide][] first and then come back here. The easiest way to run this pathogen build is using the Nextstrain command-line tool: nextstrain build . -See the [nextstrain-cli README][nextstrain-cli] for how to install the `nextstrain` command. - -Alternatively, you should be able to [run the build using `snakemake` within a -suitably-configured local environment][nextstrain-snakemake]. + Build output goes into the directories `data/`, `results/` and `auspice/`. @@ -73,9 +73,7 @@ With access to AWS, this can be more quickly run as: nextstrain build --aws-batch --aws-batch-cpus 4 --aws-batch-memory 7200 . --jobs 4 [Nextstrain]: https://nextstrain.org -[augur]: https://github.com/nextstrain/augur -[auspice]: https://github.com/nextstrain/auspice -[snakemake cli]: https://snakemake.readthedocs.io/en/stable/executable.html#all-options -[nextstrain-cli]: https://nextstrain.org/docs/getting-started/container-installation -[nextstrain-snakemake]: https://nextstrain.org/docs/getting-started/local-installation -[quickstart guide]: https://nextstrain.org/docs/getting-started/quickstart +[augur]: https://docs.nextstrain.org/projects/augur/en/stable/ +[auspice]: https://docs.nextstrain.org/projects/auspice/en/stable/index.html +[Installing Nextstrain guide]: https://docs.nextstrain.org/en/latest/install.html +[Running a Pathogen Workflow guide]: https://docs.nextstrain.org/en/latest/tutorials/running-a-workflow.html From ea709dedd89fcff411b66838730b440ad1246a7a Mon Sep 17 00:00:00 2001 From: j23414 Date: Fri, 24 Mar 2023 15:46:05 -0700 Subject: [PATCH 3/5] fix: drop comments and let the versioning software do its job --- README.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/README.md b/README.md index 25d5ea22..c645fa65 100644 --- a/README.md +++ b/README.md @@ -25,9 +25,6 @@ command-line tool: nextstrain build . - - Build output goes into the directories `data/`, `results/` and `auspice/`. Once you've run the build, you can view the results in auspice: From 7c944660d8f92398b36127d113e3712c7925a7a2 Mon Sep 17 00:00:00 2001 From: j23414 Date: Fri, 24 Mar 2023 15:49:16 -0700 Subject: [PATCH 4/5] fix: split section into GenBank and Example Datasets --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index c645fa65..62edf6e8 100644 --- a/README.md +++ b/README.md @@ -39,7 +39,7 @@ specifies its file inputs and output and also its parameters. There is little re rule should be able to be reasoned with on its own. -### GenBank vs Example Dataset +### GenBank Dataset This build starts by pulling preprocessed sequence and metadata files from: @@ -56,6 +56,8 @@ This build starts by pulling preprocessed sequence and metadata files from: The above datasets have been preprocessed and cleaned from GenBank and are updated at regular intervals. +### Example Dataset + Alternatively, you can run the build using the example data provided in this repository. Before running the build, copy the example sequences into the `data/` directory like so: From 3d198217616fd41299e258055450d87fc5b5511c Mon Sep 17 00:00:00 2001 From: j23414 Date: Fri, 24 Mar 2023 15:53:36 -0700 Subject: [PATCH 5/5] fix: match the suggested section titles --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 62edf6e8..d39ffabc 100644 --- a/README.md +++ b/README.md @@ -39,7 +39,7 @@ specifies its file inputs and output and also its parameters. There is little re rule should be able to be reasoned with on its own. -### GenBank Dataset +### Using GenBank data This build starts by pulling preprocessed sequence and metadata files from: @@ -56,7 +56,7 @@ This build starts by pulling preprocessed sequence and metadata files from: The above datasets have been preprocessed and cleaned from GenBank and are updated at regular intervals. -### Example Dataset +### Using example data Alternatively, you can run the build using the example data provided in this repository. Before running the build, copy the