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updating augur to version 26.0.0 #1054

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minor changes to dockerfile to silence warnings, quiet down some outp…
…ut, and use recommend CMD format
kapsakcj committed Nov 9, 2024
commit 80ddffc0fdeb115b17a67c8c75c64fd8eebf9141
10 changes: 5 additions & 5 deletions augur/26.0.0/Dockerfile
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
FROM python:3.11-slim as app
FROM python:3.11-slim AS app

ARG AUGUR_VER="26.0.0"

@@ -28,18 +28,18 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
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 && \
tar -xzf ${AUGUR_VER}.tar.gz && \
pip install ${AUGUR_VER}.tar.gz && \
rm ${AUGUR_VER}.tar.gz
rm -v ${AUGUR_VER}.tar.gz
#&& \
#cd augur-${AUGUR_VER} && \
#python3 -m pip install '.[full]'

CMD augur --help
CMD [ "augur", "--help" ]

WORKDIR /data

FROM app as test
FROM app AS test

RUN augur --help

22 changes: 19 additions & 3 deletions augur/26.0.0/README.md
Original file line number Diff line number Diff line change
@@ -1,6 +1,22 @@
# 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.
@@ -9,13 +25,13 @@ The output of augur is a series of JSONs that can be used to visualize your resu

Note: Auspice is a different tool.

# Example Usage
## 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 \