augur version 24.2.2 (#872)

* augur version 24.1.0

* fixed hyperlink

* update to 24.2.2

* Update to 24.2.2

* Rename README.md to README.md

README.md

@@ -113,7 +113,7 @@ 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) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/artic-ncov2019-epi2me)](https://hub.docker.com/r/staphb/artic-ncov2019-epi2me) | <ul><li>0.3.10</ul> | https://github.com/epi2me-labs/wf-artic |
 | [artic-ncov2019-medaka](https://hub.docker.com/r/staphb/artic-ncov2019-medaka) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/artic-ncov2019-medaka)](https://hub.docker.com/r/staphb/artic-ncov2019-medaka) | <ul><li>1.1.0</ul> | https://github.com/artic-network/artic-ncov2019 |
 | [artic-ncov2019-nanopolish](https://hub.docker.com/r/staphb/artic-ncov2019-nanopolish) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/artic-ncov2019-nanopolish)](https://hub.docker.com/r/staphb/artic-ncov2019-nanopolish) | <ul><li>1.1.0</ul> | https://github.com/artic-network/artic-ncov2019 |
-| [Augur](https://github.com/nextstrain/augur) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/augur)](https://hub.docker.com/r/staphb/augur) | <ul><li>6.3.0</li><li>7.0.2</li><li>8.0.0</li><li>9.0.0</li><li>16.0.3</li></ul> | https://github.com/nextstrain/augur |
+| [Augur](https://hub.docker.com/r/staphb/augur) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/augur)](https://hub.docker.com/r/staphb/augur) | <ul><li>[6.3.0](./augur/6.3.0/)</li><li>[7.0.2](./augur/7.0.2/)</li><li>[8.0.0](./augur/8.0.0/)</li><li>[9.0.0](./augur/9.0.0/)</li><li>[16.0.3](./augur/16.0.3/)</li><li>[24.2.2](./augur/24.2.2/)</li></ul> | https://github.com/nextstrain/augur |
 | [Auspice](https://hub.docker.com/r/staphb/auspice) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/auspice)](https://hub.docker.com/r/staphb/auspice) | <ul><li>2.12.0</li></ul> | https://github.com/nextstrain/auspice |
 | [bakta](https://hub.docker.com/r/staphb/bakta) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bakta)](https://hub.docker.com/r/staphb/bakta) | <ul><li>[1.9.2](./bakta/1.9.2/)</li><li>[1.9.2-light](./bakta/1.9.2-5.1-light/)</li></ul> | https://github.com/oschwengers/bakta |
 | [BBTools](https://hub.docker.com/r/staphb/bbtools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bbtools)](https://hub.docker.com/r/staphb/bbtools) | <ul><li>38.76</li><li>38.86</li><li>38.95</li><li>38.96</li><li>38.97</li><li>38.98</li><li>38.99</li><li>39.00</li><li>39.01</li></ul> | https://jgi.doe.gov/data-and-tools/bbtools/ |

augur/24.2.2/Dockerfile

@@ -0,0 +1,63 @@
+FROM python:3.11-slim as app
+
+ARG AUGUR_VER="24.2.2"
+
+# 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=${AUGUR_VER}
+LABEL description="Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data.The output of augur is a series of JSONs that can be used to visualize your results using Auspice."
+LABEL website="https://github.com/nextstrain/augur"
+LABEL license="https://github.com/nextstrain/augur/blob/master/LICENSE.txt"
+LABEL maintainer="John Arnn"
+LABEL maintainer.email="[email protected]"
+
+# 'RUN' executes code during the build
+# Install dependencies via apt-get or yum if using a centos or fedora base
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    procps \
+    ca-certificates \
+    wget \
+    mafft \
+    iqtree \
+    raxml \
+    fasttree  \
+    vcftools && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN wget -q https://github.com/nextstrain/augur/archive/refs/tags/${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

augur/24.2.2/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)