updating augur to version 26.0.0

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) <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 |
 | [assembly_snptyper](https://hub.docker.com/r/staphb/assembly_snptyperh) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/assembly_snptyper)](https://hub.docker.com/r/staphb/assembly_snptyper) | <ul><li>[0.1.1](./assembly_snptyper/0.1.1/)</li></ul> | https://github.com/boasvdp/assembly_snptyper |
-| [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><li>[24.2.3](./augur/24.2.3/)</li><li>[24.3.0](./augur/24.3.0/)</li><li>[24.4.0](./augur/24.4.0/)</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><li>[24.2.3](./augur/24.2.3/)</li><li>[24.3.0](./augur/24.3.0/)</li><li>[24.4.0](./augur/24.4.0/)</li><li>[26.0.0](./augur/26.0.0/)</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><li>[1.9.3](./bakta/1.9.3/)</li><li>[1.9.3-light](./bakta/1.9.3-5.1-light/)</li><li>[1.9.4](./bakta/1.9.4/)</li><li>[1.9.4-5.1-light](./bakta/1.9.4-5.1-light/)</ul> | https://github.com/oschwengers/bakta |
 | [bandage](https://hub.docker.com/r/staphb/bandage) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bandage)](https://hub.docker.com/r/staphb/bandage) | <ul><li>[0.8.1](./bandage/0.8.1/)</li></ul> | https://rrwick.github.io/Bandage/ |

augur/26.0.0/Dockerfile

@@ -0,0 +1,65 @@
+FROM python:3.11-slim AS app
+
+ARG AUGUR_VER="26.0.0"
+
+# 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=${AUGUR_VER}
+LABEL description="Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data.The output of augur is a series of JSONs that can be used to visualize your results using Auspice."
+LABEL website="https://github.com/nextstrain/augur"
+LABEL license="https://github.com/nextstrain/augur/blob/master/LICENSE.txt"
+LABEL maintainer="John Arnn"
+LABEL maintainer.email="[email protected]"
+
+# 'RUN' executes code during the build
+# Install dependencies via apt-get or yum if using a centos or fedora base
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    procps \
+    ca-certificates \
+    wget \
+    mafft \
+    iqtree \
+    raxml \
+    fasttree  \
+    vcftools && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN wget -q https://github.com/nextstrain/augur/archive/refs/tags/${AUGUR_VER}.tar.gz && \
+    tar -xzf ${AUGUR_VER}.tar.gz && \
+    pip install ${AUGUR_VER}.tar.gz && \
+    rm -v ${AUGUR_VER}.tar.gz 
+    #&& \
+    #cd augur-${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/26.0.0/README.md

@@ -0,0 +1,46 @@
+# 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
+- biopython 1.84
+- matplotlib 3.9.2
+- numpy 1.26.4
+- pandas 1.5.3
+- phylo-treetime 0.11.4
+- python 3.11.10
+- scipy 1.14.1
+
+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)