adding virulencefinder version 3.0.0

[erinyoung]

There's a new version of virulencefinder!

Admittedly, I am unclear what is new in this version, but I'm sure there are some bug fixes or new features.

When I went about updating the Dockerfile, I did attempt to update the base image to ubuntu:jammy. This resulted in python incompatibilities issues (ubuntu:jammy's default python 3 is 3.10) among other errors.

Therefore, I kept everything in the prior dockerfile and updated the software version, database version, and kma version. I also added a CMD line and changed the tabs.

The differences between 2.0.4 and 2.0.5:

$ diff virulencefinder/2.0.4/Dockerfile virulencefinder/2.0.5/Dockerfile 
1,4c1,4
< ARG VIRULENCEFINDER_VER="2.0.1"
< # Database not properly versioned, so using most recent commit made on 2023-05-03
< # see here: https://bitbucket.org/genomicepidemiology/virulencefinder_db/commits/f678bdc15283aed3a45f66050d2eb3a6c9651f3f
< ARG VIRULENCEFINDER_DB_COMMIT_HASH="f678bdc15283aed3a45f66050d2eb3a6c9651f3f"
---
> ARG VIRULENCEFINDER_VER="2.0.5"
> # Database not properly versioned, so using most recent commit made on 2024-01-02
> # see here: https://bitbucket.org/genomicepidemiology/virulencefinder_db/commits/2b705359191a24f6db64f891ab07c93b0281e685
> ARG VIRULENCEFINDER_DB_COMMIT_HASH="2b705359191a24f6db64f891ab07c93b0281e685"
10a11
> ARG KMA_VER="1.4.14"
24c25
< # ncbi-blast+ v2.9.0 (ubuntu:focal), min required version is 2.8.1
---
> # ncbi-blast+ v2.9.0-2 (ubuntu:focal), min required version is 2.8.1
27,41c28,42
<  wget \
<  ca-certificates \
<  procps \
<  git \
<  ncbi-blast+ \
<  python3 \
<  python3-pip \
<  python3-setuptools \
<  python3-dev \
<  gcc \
<  make \
<  libz-dev \
<  dos2unix \
<  unzip && \
<  apt-get autoclean && rm -rf /var/lib/apt/lists/*
---
>     wget \
>     ca-certificates \
>     procps \
>     git \
>     ncbi-blast+ \
>     python3 \
>     python3-pip \
>     python3-setuptools \
>     python3-dev \
>     gcc \
>     make \
>     libz-dev \
>     dos2unix \
>     unzip && \
>     apt-get autoclean && rm -rf /var/lib/apt/lists/*
48,51c49,52
< RUN git clone --branch 1.0.1 --depth 1 https://bitbucket.org/genomicepidemiology/kma.git && \
<  cd kma && \
<  make && \
<  mv -v kma* /usr/local/bin/
---
> RUN git clone --branch ${KMA_VER} --depth 1 https://bitbucket.org/genomicepidemiology/kma.git && \
>     cd kma &&\
>     make &&\
>     mv kma kma_index kma_shm kma_update /usr/local/bin/
58,62c59,63
<  git clone https://bitbucket.org/genomicepidemiology/virulencefinder_db.git /database && \
<  cd /database && \
<  git checkout ${VIRULENCEFINDER_DB_COMMIT_HASH} && \
<  dos2unix *.fsa && \
<  python3 INSTALL.py kma_index
---
>     git clone https://bitbucket.org/genomicepidemiology/virulencefinder_db.git /database && \
>     cd /database && \
>     git checkout ${VIRULENCEFINDER_DB_COMMIT_HASH} && \
>     dos2unix *.fsa && \
>     python3 INSTALL.py kma_index
66c67
<  mkdir /data
---
>     mkdir /data
70c71
<  LC_ALL=C.UTF-8
---
>     LC_ALL=C.UTF-8
80a82,83
> RUN virulencefinder.py -h
> 
89,92c92,95
<  wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/012/224/845/GCA_012224845.2_ASM1222484v2/GCA_012224845.2_ASM1222484v2_genomic.fna.gz && \
<  gunzip GCA_012224845.2_ASM1222484v2_genomic.fna.gz && \
<  virulencefinder.py -i /test/GCA_012224845.2_ASM1222484v2_genomic.fna -x -o /test/asm-input && \
<  cat /test/asm-input/results_tab.tsv
---
>     wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/012/224/845/GCA_012224845.2_ASM1222484v2/GCA_012224845.2_ASM1222484v2_genomic.fna.gz && \
>     gunzip GCA_012224845.2_ASM1222484v2_genomic.fna.gz && \
>     virulencefinder.py -i /test/GCA_012224845.2_ASM1222484v2_genomic.fna -x -o /test/asm-input && \
>     cat /test/asm-input/results_tab.tsv
96,98c99,101
<  wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR690/006/SRR6903006/SRR6903006_1.fastq.gz && \
<  virulencefinder.py -i SRR6903006_1.fastq.gz -mp kma -x -o /test/reads-input && \
<  cat /test/reads-input/results_tab.tsv
---
>     wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR690/006/SRR6903006/SRR6903006_1.fastq.gz && \
>     virulencefinder.py -i SRR6903006_1.fastq.gz -mp kma -x -o /test/reads-input && \
>     cat /test/reads-input/results_tab.tsv
104,105c107,108
<  virulencefinder.py -i test.fsa -o . -mp blastn -x -q && \
<  virulencefinder.py --help
---
>     virulencefinder.py -i test.fsa -o . -mp blastn -x -q && \
>     virulencefinder.py --help

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

[kapsakcj]

I betcha the database has been updated with new/recently designated shiga toxin subtypes (and maybe other updates too)

[kapsakcj]

I won't be able to review this week, but don't let that stop others from reviewing if they have the time

[erinyoung]

I went to check on this PR, and it looks like there are some changes being made to the virulencefinder_db (https://bitbucket.org/genomicepidemiology/virulencefinder_db/commits/). I want to give those some time to settle.

[erinyoung]

I've updated the database commit hash. It looks like the last commit was at the beginning of April, so this is probably safe to review now.

[erinyoung]

@kapsakcj , it appears that version 3.0.0 came out the other day. It's similar to resfinder.

I've changed the tool specific readme drastically. Let me know if something is unclear.