Update Augur to 16.0.3

[jwarnn]

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Hello; I need an updated augur tool for making a Nextflow workflow for Nextstrain. Augur needs a version of python that is 3.7 or greater; apt-get downloads python 3.6.something. I download and install python from source because of this issue. I also do not download pip with apt-get because I want to make sure that the pip is compatible with the version of python that I already installed. The rest is pretty standard. Thanks.

Pull Request (PR) checklist:

• [X] Include a description of what is in this pull request in this message.
• [X] The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
• [X] Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
  • [ ] (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
• [X] Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
  • [ ] If this README is longer than 30 lines, there is an explanation as to why more detail was needed
• [X] Dockerfile includes the recommended LABELS
• [X] Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• [X] Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

[erinyoung]

This dockerfile looks very different from the prior version. This isn't a bad thing, it looks like augur has undergone a lot of changes, so it makes sense that the dockerfile would be different.

Things installed in v.9 (https://github.com/StaPH-B/docker-builds/blob/master/augur/9.0.0/Dockerfile)

• python3
• wget
• python3-pip
• iqtree=1.6.1+dfsg-1
• build-essential
• zlib1g-dev
• pkg-config
• mafft=7.310-1
• locales
• vcftools
• nextstrain-augur
• snakemake

In version 16 :

• wget
• build-essential
• zlib1g-dev
• libncurses5-dev
• libgdbm-dev
• libnss3-dev
• libssl-dev
• libreadline-dev
• libffi-dev
• libsqlite3-dev
• libbz2-dev
• liblzma-dev
• pkg-config
• libpng-dev
• libfreetype6-dev
• git
• Python-3.8.0
• pip3
• pip
• Cython

And so far it looks fine.

According to nextstrain's installation instructions at https://docs.nextstrain.org/projects/augur/en/stable/installation/installation.html, the following are also needed:

• snakemake (for the tutorials)
• mafft
• iqtree (I wonder if they mean iqtree2)
• raxml
• fasttree
• vcftools

Could you add these?

[jwarnn]

I like the more robust test and this is how I would implement it:

FROM app as test

RUN pip3 install snakemake

RUN git clone https://github.com/nextstrain/zika-tutorial && \
    cd zika-tutorial && \
    snakemake --cores 1

I thought since snakemake will only be used in the test I wanted to keep it out of the app part of the build.

Also for the additional packages should we include versions? If yes; should I just use the minimum that is suggested in the Augur documentation? :

libfreetype6-dev \
  mafft python2.7- \
  iqtree \
  raxml \
  fasttree  \
  vcftools \
  git && \

Thanks!

[jwarnn]

Looking at the bioconda recipe; it does not specify versions for those tools.

[jwarnn]

Added tools and more robust test to Dockerfile.

[erinyoung]

Looks good! I'm going to

1. merge this
2. send this to dockerhub and quay
3. overwrite the latest tag

This should be done momentarily! Thank you!