adding piranha version 1.4.2

[erinyoung]

There's a new version of piranha! (Well... a few of them)

According to the release notes there are more minimap2 options.

I copied the files from 1.0.4 and made some changes

• base changed to mambaorg/micromamba:2.0.5-ubuntu22.04
• updated version ARG
• adjusted how pip installs piranha
• install pyabpoa with pip to suppress warning (likely a medaka thing)
• adjusted paths in test
• added conda install to path so that mamba environmental variables aren't needed
• added CMD line
• fixed website URL
• adjusted tabs for my linter
• changed as to AS for my linter

The full diff:

$ diff build-files/piranha/1.*/Dockerfile
1c1,5
< FROM mambaorg/micromamba:0.27.0 as app
---
> ARG PIRANHA_VER="1.4.2"
> 
> FROM mambaorg/micromamba:2.0.5-ubuntu22.04 AS app
> 
> ARG PIRANHA_VER
8,10d11
< # ARG variables only persist during build time
< ARG PIRANHA_VER="1.0.4"
< 
12c13
< LABEL base.image="mambaorg/micromamba:0.27.0"
---
> LABEL base.image="mambaorg/micromamba:2.0.5-ubuntu22.04"
17c18
< LABEL website="https://github.com/cov-lineages/piranha"
---
> LABEL website="https://github.com/polio-nanopore/piranha"
20,21c21,22
< LABEL maintainer1="Curtis Kapsak"
< LABEL maintainer1.email="curtis.kapsak@theiagen.com"
---
> LABEL maintainer="Curtis Kapsak"
> LABEL maintainer.email="curtis.kapsak@theiagen.com"
27,32c28,32
<  wget \
<  ca-certificates \
<  git \
<  procps \
<  build-essential && \
<  apt-get autoclean && rm -rf /var/lib/apt/lists/*
---
>     wget \
>     ca-certificates \
>     procps \
>     build-essential && \
>     apt-get autoclean && rm -rf /var/lib/apt/lists/*
35,56c35,40
< RUN wget "https://github.com/polio-nanopore/piranha/archive/refs/tags/${PIRANHA_VER}.tar.gz" && \
<  tar -xf ${PIRANHA_VER}.tar.gz && \
<  rm ${PIRANHA_VER}.tar.gz && \
<  mv -v piranha-* piranha && \
<  micromamba create -n piranha -y -f /piranha/environment.yml
< 
< # set the environment; PATH unneccessary at this point, for easy changes later; LC_ALL is for singularity compatibility
< ENV PATH="${PATH}" \
<  LC_ALL=C.UTF-8
< 
< # so that mamba/conda env is active when running below commands
< ENV ENV_NAME="piranha"
< ARG MAMBA_DOCKERFILE_ACTIVATE=1
< 
< WORKDIR /piranha
< 
< # run pip install step
< # clean up micromamba/conda garbage
< # make /data directory
< RUN pip install . && \
<  micromamba clean -a -y && \
<  mkdir /data 
---
> RUN wget -q https://github.com/polio-nanopore/piranha/archive/refs/tags/${PIRANHA_VER}.tar.gz && \
>     tar -xf ${PIRANHA_VER}.tar.gz && \
>     micromamba create -n piranha -y -f /piranha-${PIRANHA_VER}/environment.yml && \
>     /opt/conda/envs/piranha/bin/pip install ${PIRANHA_VER}.tar.gz --no-cache-dir && \
>     rm ${PIRANHA_VER}.tar.gz && \
>     mkdir /data 
62c46,51
< ENV PATH="${PATH}:/opt/conda/envs/piranha/bin/"
---
> ENV PATH="${PATH}:/opt/conda/envs/piranha/bin/" \
>     LC_ALL=C.UTF-8
> 
> RUN pip install pyabpoa
> 
> CMD ["piranha" ,"--help"]
65c54
< FROM app as test
---
> FROM app AS test
67,69c56
< # # so that mamba/conda env is active when running below commands
< ENV ENV_NAME="piranha"
< ARG MAMBA_DOCKERFILE_ACTIVATE=1
---
> ARG PIRANHA_VER
75c62
< WORKDIR /piranha
---
> WORKDIR /test
80,81c67,68
< RUN piranha -i piranha/test/pak_run/demultiplexed --verbose -b piranha/test/pak_run/barcodes01.csv -t 2 2>&1 | tee piranha.log && \
<  piranha -i piranha/test/pak_run/demultiplexed --verbose -b piranha/test/pak_run/barcodes.csv -t 2 2>&1 | tee piranha_all.log
---
> RUN piranha -i /piranha-${PIRANHA_VER}/piranha/test/pak_run/demultiplexed --verbose -b /piranha-${PIRANHA_VER}/piranha/test/pak_run/barcodes01.csv -t 2 2>&1 | tee piranha.log && \
>     piranha -i /piranha-${PIRANHA_VER}/piranha/test/pak_run/demultiplexed --verbose -b /piranha-${PIRANHA_VER}/piranha/test/pak_run/barcodes.csv -t 2 2>&1 | tee piranha_all.log

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• 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/build-files/samtools/1.15 )
• Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number in build-files (i.e. docker-builds/build-files/spades/3.12.0/Dockerfile)
  • (optional) All test files are located in same directory as the Dockerfile (i.e. build-files/shigatyper/2.0.1/test.sh)
• Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. docker-builds/build-files/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
• Dockerfile includes the recommended LABELS
• Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

[kapsakcj]

everything looks good and the tests passed. They did take 10 min, but not much we can do about that 🤷

I'm going to merge and deploy

[kapsakcj]

deploy workflow here: https://github.com/StaPH-B/docker-builds/actions/runs/13961562371

thank you for the PR!