adding spades version 4.0.0

[erinyoung]

There's a new version of spades!

According to the release notes there are a lot more options, specifically with assembly graphs.

I copied the files from 3.15.5 and made the following changes:

1. updated the base image to jammy
2. updated the version arg
3. messed with the tabs
4. added libgomp1 to the apt-get layer
5. added CMD layer

 $ diff spades/3.15.5/Dockerfile spades/4.0.0/Dockerfile 
1c1
< FROM ubuntu:focal as app
---
> FROM ubuntu:jammy as app
4c4
< ARG SPADES_VER="3.15.5"
---
> ARG SPADES_VER="4.0.0"
6,7c6,7
< LABEL base.image="ubuntu:focal"
< LABEL dockerfile.version="2"
---
> LABEL base.image="ubuntu:jammy"
> LABEL dockerfile.version="1"
18,24c18,26
< RUN apt-get update && apt-get install --no-install-recommends -y python3 \
<  python3-distutils \
<  wget \
<  pigz \
<  ca-certificates && \
<  apt-get autoclean && rm -rf /var/lib/apt/lists/* && \
<  update-alternatives --install /usr/bin/python python /usr/bin/python3 10
---
> RUN apt-get update && apt-get install --no-install-recommends -y \
>   python3 \
>   python3-distutils \
>   wget \
>   pigz \
>   ca-certificates \
>   libgomp1 && \
>   apt-get autoclean && rm -rf /var/lib/apt/lists/* && \
>   update-alternatives --install /usr/bin/python python /usr/bin/python3 10
27c29
< RUN wget http://cab.spbu.ru/files/release${SPADES_VER}/SPAdes-${SPADES_VER}-Linux.tar.gz && \
---
> RUN wget -q https://github.com/ablab/spades/releases/download/v${SPADES_VER}/SPAdes-${SPADES_VER}-Linux.tar.gz && \
34c36
<     PATH="${PATH}:/SPAdes-${SPADES_VER}-Linux/bin"
---
>   PATH="${PATH}:/SPAdes-${SPADES_VER}-Linux/bin"
42c44,47
< RUN spades.py --version && spades.py --test && spades.py --help
---
> RUN spades.py --version && spades.py --help
> 
> # run the supplied test
> RUN spades.py --test

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)
  • [X] (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)
  • [X] 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

[Kincekara]

Thank you for the update! It seems there are a lot of changes in spades. Deploy link: https://github.com/StaPH-B/docker-builds/actions/runs/9668878536