From 10ea3027c9edaecef786319f30e8a45421c1184f Mon Sep 17 00:00:00 2001 From: Erin Young Date: Wed, 18 Dec 2024 23:44:11 +0000 Subject: [PATCH] adding augur version 27.0.0 --- README.md | 2 +- augur/27.0.0/Dockerfile | 62 +++++++++++++++++++++++++++++++++++++++++ augur/27.0.0/README.md | 40 ++++++++++++++++++++++++++ 3 files changed, 103 insertions(+), 1 deletion(-) create mode 100644 augur/27.0.0/Dockerfile create mode 100644 augur/27.0.0/README.md diff --git a/README.md b/README.md index f435e9475..306d92966 100644 --- a/README.md +++ b/README.md @@ -120,7 +120,7 @@ To learn more about the docker pull rate limits and the open source software pro | [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 | | [assembly_snptyper](https://hub.docker.com/r/staphb/assembly_snptyperh)
[![docker pulls](https://badgen.net/docker/pulls/staphb/assembly_snptyper)](https://hub.docker.com/r/staphb/assembly_snptyper) | | https://github.com/boasvdp/assembly_snptyper | -| [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/27.0.0/Dockerfile b/augur/27.0.0/Dockerfile new file mode 100644 index 000000000..7cefbe234 --- /dev/null +++ b/augur/27.0.0/Dockerfile @@ -0,0 +1,62 @@ +FROM python:3.11-slim AS app + +ARG AUGUR_VER="27.0.0" + +# 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 -xzf ${AUGUR_VER}.tar.gz && \ + pip install ${AUGUR_VER}.tar.gz && \ + rm -v ${AUGUR_VER}.tar.gz + +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/27.0.0/README.md b/augur/27.0.0/README.md new file mode 100644 index 000000000..3a514d266 --- /dev/null +++ b/augur/27.0.0/README.md @@ -0,0 +1,40 @@ +# Augur Container + +Main tool: [Augur](https://github.com/nextstrain/augur) + +Additional tools: + +- mafft 7.505 +- iqtree2 2.0.7 +- raxml 8.2.12 +- fasttree 2.1.11 +- vcftools 0.1.16 + + +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 + +```bash +augur index --sequences sequences.fasta --output sequence_index.tsv +``` + +```bash +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)