From 2da1bd10b3d1ef475b5d6b8d2a1dd03edf8331d7 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 2 Jul 2024 13:32:37 -0600 Subject: [PATCH] augur version 24.4.0 (#989) * augur version 24.4.0 * augur version 24.4.0 --- README.md | 2 +- augur/24.4.0/Dockerfile | 63 +++++++++++++++++++++++++++++++++++++++++ augur/24.4.0/README.md | 30 ++++++++++++++++++++ 3 files changed, 94 insertions(+), 1 deletion(-) create mode 100644 augur/24.4.0/Dockerfile create mode 100644 augur/24.4.0/README.md diff --git a/README.md b/README.md index b007f3d9b..49962974d 100644 --- a/README.md +++ b/README.md @@ -114,7 +114,7 @@ To learn more about the docker pull rate limits and the open source software pro | [artic-ncov2019-epi2me](https://hub.docker.com/r/staphb/artic-ncov2019-epi2me)
[![docker pulls](https://badgen.net/docker/pulls/staphb/artic-ncov2019-epi2me)](https://hub.docker.com/r/staphb/artic-ncov2019-epi2me) | | https://github.com/epi2me-labs/wf-artic | | [artic-ncov2019-medaka](https://hub.docker.com/r/staphb/artic-ncov2019-medaka)
[![docker pulls](https://badgen.net/docker/pulls/staphb/artic-ncov2019-medaka)](https://hub.docker.com/r/staphb/artic-ncov2019-medaka) | | https://github.com/artic-network/artic-ncov2019 | | [artic-ncov2019-nanopolish](https://hub.docker.com/r/staphb/artic-ncov2019-nanopolish)
[![docker pulls](https://badgen.net/docker/pulls/staphb/artic-ncov2019-nanopolish)](https://hub.docker.com/r/staphb/artic-ncov2019-nanopolish) | | https://github.com/artic-network/artic-ncov2019 | -| [Augur](https://hub.docker.com/r/staphb/augur)
[![docker pulls](https://badgen.net/docker/pulls/staphb/augur)](https://hub.docker.com/r/staphb/augur) | | https://github.com/nextstrain/augur | +| [Augur](https://hub.docker.com/r/staphb/augur)
[![docker pulls](https://badgen.net/docker/pulls/staphb/augur)](https://hub.docker.com/r/staphb/augur) | | https://github.com/nextstrain/augur | | [Auspice](https://hub.docker.com/r/staphb/auspice)
[![docker pulls](https://badgen.net/docker/pulls/staphb/auspice)](https://hub.docker.com/r/staphb/auspice) | | https://github.com/nextstrain/auspice | | [bakta](https://hub.docker.com/r/staphb/bakta)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bakta)](https://hub.docker.com/r/staphb/bakta) | | https://github.com/oschwengers/bakta | | [bandage](https://hub.docker.com/r/staphb/bandage)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bandage)](https://hub.docker.com/r/staphb/bandage) | | https://rrwick.github.io/Bandage/ | diff --git a/augur/24.4.0/Dockerfile b/augur/24.4.0/Dockerfile new file mode 100644 index 000000000..639ff75e2 --- /dev/null +++ b/augur/24.4.0/Dockerfile @@ -0,0 +1,63 @@ +FROM python:3.11-slim as app + +ARG AUGUR_VER="24.4.0" + +# LABEL instructions tag the image with metadata that might be important to the user +# Optional, but highly recommended +LABEL base.image="python:3.11-slim" +LABEL dockerfile.version="1" +LABEL software="augur" +LABEL software.version=${AUGUR_VER} +LABEL description="Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data.The output of augur is a series of JSONs that can be used to visualize your results using Auspice." +LABEL website="https://github.com/nextstrain/augur" +LABEL license="https://github.com/nextstrain/augur/blob/master/LICENSE.txt" +LABEL maintainer="John Arnn" +LABEL maintainer.email="jarnn@utah.gov" + +# 'RUN' executes code during the build +# Install dependencies via apt-get or yum if using a centos or fedora base +RUN apt-get update && apt-get install -y --no-install-recommends \ + procps \ + ca-certificates \ + wget \ + mafft \ + iqtree \ + raxml \ + fasttree \ + vcftools && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +RUN wget -q https://github.com/nextstrain/augur/archive/refs/tags/${AUGUR_VER}.tar.gz && \ + tar -xzvf ${AUGUR_VER}.tar.gz && \ + rm ${AUGUR_VER}.tar.gz && \ + cd augur-${AUGUR_VER} && \ + python3 -m pip install '.[full]' + +CMD augur --help + +WORKDIR /data + +FROM app as test + +RUN augur --help + +WORKDIR /test + +RUN apt-get update && apt-get install -y --no-install-recommends git + +RUN git clone https://github.com/nextstrain/zika-tutorial && \ + cd zika-tutorial && \ + mkdir results && \ + augur index --sequences data/sequences.fasta --output results/sequence_index.tsv && \ + augur filter --sequences data/sequences.fasta \ + --sequence-index results/sequence_index.tsv \ + --metadata data/metadata.tsv \ + --exclude config/dropped_strains.txt \ + --output results/filtered.fasta \ + --sequences-per-group 20 \ + --min-date 2012 && \ + augur align \ + --sequences results/filtered.fasta \ + --reference-sequence config/zika_outgroup.gb \ + --output results/aligned.fasta \ + --fill-gaps diff --git a/augur/24.4.0/README.md b/augur/24.4.0/README.md new file mode 100644 index 000000000..f8c0ee80c --- /dev/null +++ b/augur/24.4.0/README.md @@ -0,0 +1,30 @@ +# Augur Container +Main tool: [Augur](https://github.com/nextstrain/augur) + +Definition: One held to foretell events by omens. + +Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data. It provides a collection of commands which are designed to be composable into larger processing pipelines. + +The output of augur is a series of JSONs that can be used to visualize your results using Auspice. + +Note: Auspice is a different tool. + +# Example Usage + +``` +augur index --sequences sequences.fasta --output sequence_index.tsv +``` + +``` +augur filter \ + --sequences data/sequences.fasta \ + --sequence-index results/sequence_index.tsv \ + --metadata data/metadata.tsv \ + --exclude config/dropped_strains.txt \ + --output results/filtered.fasta \ + --group-by country year month \ + --sequences-per-group 20 \ + --min-date 2012 +``` + +Better documentation can be found [here.](https://docs.nextstrain.org/en/latest/tutorials/creating-a-workflow.html)