Adding spades version 4.1.0

[erinyoung]

There's a new version of spades!

According to the release notes this version has some performance improvements.

I copied the files from 4.0.0, updated the version ARG, changed the format of the CMD and FROM lines (for my linter), and added a test layer using real data.

The full diff:

$ diff build-files/spades/4*/Dockerfile
1c1
< FROM ubuntu:jammy as app
---
> FROM ubuntu:jammy AS app
4c4
< ARG SPADES_VER="4.0.0"
---
> ARG SPADES_VER="4.1.0"
38c38
< CMD spades.py --help
---
> CMD ["spades.py", "--help"]
43c43
< FROM app as test
---
> FROM app AS test
49a50,57
> 
> WORKDIR /test
> 
> # run on some test files
> RUN wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR323/020/SRR32343420/SRR32343420_1.fastq.gz && \
>   wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR323/020/SRR32343420/SRR32343420_2.fastq.gz && \
>   spades.py --isolate -1 SRR32343420_1.fastq.gz -2 SRR32343420_2.fastq.gz --threads 4 -o test && \
>   head /test/test/contigs.fasta
\ No newline at end of file

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

[Kincekara]

Could you change the license in the docker file and program_licences.md with https://github.com/ablab/spades/blob/main/LICENSE

[Kincekara]

I didn't want to hold this PR too long, so I changed the license label in the dockerfile. I will handle programs_licenses.md later.

[Kincekara]

Thank you for the update!
Deploy link: https://github.com/StaPH-B/docker-builds/actions/runs/13705997903

[erinyoung]

Sorry for taking so long to circle back to this! Thank you for taking care of it!!!