-
Notifications
You must be signed in to change notification settings - Fork 119
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* augur version 24.4.0 * augur version 24.4.0
- Loading branch information
Showing
3 changed files
with
94 additions
and
1 deletion.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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=${AUGUR_VER} | ||
| LABEL description="Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data.The output of augur is a series of JSONs that can be used to visualize your results using Auspice." | ||
| LABEL website="https://github.com/nextstrain/augur" | ||
| LABEL license="https://github.com/nextstrain/augur/blob/master/LICENSE.txt" | ||
| LABEL maintainer="John Arnn" | ||
| LABEL maintainer.email="[email protected]" | ||
|
|
||
| # 'RUN' executes code during the build | ||
| # Install dependencies via apt-get or yum if using a centos or fedora base | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| procps \ | ||
| ca-certificates \ | ||
| wget \ | ||
| mafft \ | ||
| iqtree \ | ||
| raxml \ | ||
| fasttree \ | ||
| vcftools && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
|
|
||
| RUN wget -q https://github.com/nextstrain/augur/archive/refs/tags/${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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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) |