adding virulencefinder version 3.0.0 #927
Conversation
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I betcha the database has been updated with new/recently designated shiga toxin subtypes (and maybe other updates too) |
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I won't be able to review this week, but don't let that stop others from reviewing if they have the time |
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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. |
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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
changed the title
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@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. |
want to silence warning and trigger automation to build
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Sorry for taking so dang long to finally review. I'm making a few changes to the dockerfile to improve some aspects. According to this file: https://bitbucket.org/genomicepidemiology/virulencefinder/src/master/pyproject.toml biopython 1.79 or higher is installed, cgecore 1.5.6 is installed, and tabulate 0.8.9 are installed, so I'm going to test out removing the EDIT: yep, that line was unnecessary and confusing so I removed it. those python packages are installed alongside virulencefinder |
…der 3.0.0 dockerfile
…ker-builds into erin-virulencefinder
…h shell so alias is set properly (I was getting a weird error when running the virulencefinder.py command manually
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@erinyoung OK I believe I'm done making changes. Here's the updated $ diff -w virulencefinder/2.0.4/Dockerfile virulencefinder/3.0.0/Dockerfile
1,4c1,5
< 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="3.0.0"
> ARG VIRULENCEFINDER_DB_VER="2.0.0"
> # Database sometimes is not properly versioned, so using most recent commit made on 2024-04-06 would be something like
> # see here: https://bitbucket.org/genomicepidemiology/virulencefinder_db/commits/bcf7f0b26271a59ca85715fa2ab8a0c380e5357b
> # ARG VIRULENCEFINDER_DB_COMMIT_HASH="bcf7f0b26271a59ca85715fa2ab8a0c380e5357b"
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< FROM ubuntu:focal as app
---
> FROM ubuntu:jammy AS app
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> ARG VIRULENCEFINDER_DB_VER
> ARG KMA_VER="1.4.15"
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< LABEL base.image="ubuntu:focal"
---
> LABEL base.image="ubuntu:jammy"
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< LABEL website="https://bitbucket.org/genomicepidemiology/virulencefinder/src/master/"
---
> LABEL website="https://bitbucket.org/genomicepidemiology/virulencefinder"
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> LABEL maintainer1="Erin Young"
> LABEL maintainer1.email="[email protected]"
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< # ncbi-blast+ v2.9.0 (ubuntu:focal), min required version is 2.8.1
< # python3 v3.8.10, min required version is 3.5
---
> # ncbi-blast+ v2.12.0 (ubuntu:jammy), min required version is 2.8.1
> # python3 v3.10.12, min required version is 3.10
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< unzip && \
< apt-get autoclean && rm -rf /var/lib/apt/lists/*
<
< # install python dependencies
< RUN pip3 install biopython==1.73 tabulate==0.7.7 cgecore==1.5.5
---
> unzip \
> python-is-python3 && \
> apt-get autoclean && rm -rf /var/lib/apt/lists/* && \
> update-alternatives --install /usr/bin/python python /usr/bin/python3 10
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< RUN git clone --branch 1.0.1 --depth 1 https://bitbucket.org/genomicepidemiology/kma.git && \
---
> RUN git clone --branch ${KMA_VER} --depth 1 https://bitbucket.org/genomicepidemiology/kma.git && \
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< mv -v kma* /usr/local/bin/
---
> mv kma kma_index kma_shm kma_update /usr/local/bin/
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< # download VIRULENCEFINDER database using a specific commit hash to aid in reproducibility
---
> # download VIRULENCEFINDER database
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< # NOTE: files HAVE to go into '/database' since that is the default location expected by serotyperfinder.py
---
> # NOTE: files HAVE to go into '/database' since that is the default location expected by virulencefinder
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< git clone https://bitbucket.org/genomicepidemiology/virulencefinder_db.git /database && \
< cd /database && \
< git checkout ${VIRULENCEFINDER_DB_COMMIT_HASH} && \
---
> git clone --depth 1 https://bitbucket.org/genomicepidemiology/virulencefinder_db.git /databases && \
> cd /databases && \
> git fetch --depth 1 origin tag ${VIRULENCEFINDER_DB_VER} && \
> rm -rf .git && \
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< RUN git clone --branch ${VIRULENCEFINDER_VER} https://bitbucket.org/genomicepidemiology/virulencefinder.git && \
---
> RUN git clone --branch ${VIRULENCEFINDER_VER} --depth 1 https://bitbucket.org/genomicepidemiology/virulencefinder.git && \
> rm -rf /virulencefinder/.git && \
> cd /virulencefinder && \
> pip3 install . && \
70c78,80
< LC_ALL=C.UTF-8
---
> LC_ALL=C.UTF-8 \
> CGE_BLASTN=/usr/bin/blastn \
> CGE_VIRULENCEFINDER_DB=/databases
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> # force bash shell so below lines to make an alias runs properly
> SHELL ["/bin/bash", "-c"]
>
> # setting a janky alias for everyone that uses the "latest" tag
> RUN echo -e '#!/bin/bash\npython -m virulencefinder "$@"' > /usr/bin/virulencefinder.py && \
> chmod +x /usr/bin/virulencefinder.py
>
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< CMD [ "virulencefinder.py", "-h"]
---
> CMD [ "python", "-m", "virulencefinder", "-h" ]
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< FROM app as test
---
> FROM app AS test
>
> RUN python -m virulencefinder -h && /usr/bin/virulencefinder.py -h
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< RUN mkdir -v /test/asm-input && \
< wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/012/224/845/GCA_012224845.2_ASM1222484v2/GCA_012224845.2_ASM1222484v2_genomic.fna.gz && \
---
> RUN mkdir asm-input && \
> wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/012/224/845/GCA_012224845.2_ASM1222484v2/GCA_012224845.2_ASM1222484v2_genomic.fna.gz && \
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< virulencefinder.py -i /test/GCA_012224845.2_ASM1222484v2_genomic.fna -x -o /test/asm-input && \
< cat /test/asm-input/results_tab.tsv
---
> python -m virulencefinder -h && \
> which blastn && \
> head -n 5 /test/GCA_012224845.2_ASM1222484v2_genomic.fna && \
> python -m virulencefinder -ifa /test/GCA_012224845.2_ASM1222484v2_genomic.fna --extented_output -o asm-input && \
> ls asm-input && \
> cat asm-input/results_tab.tsv
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< 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 && \
---
> wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR690/006/SRR6903006/SRR6903006_1.fastq.gz && \
> wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR690/006/SRR6903006/SRR6903006_2.fastq.gz && \
> python -m virulencefinder -ifq SRR6903006_1.fastq.gz SRR6903006_2.fastq.gz --extented_output -o /test/reads-input && \
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< RUN cd /virulencefinder/test && \
< virulencefinder.py -i test.fsa -o . -mp blastn -x -q && \
< virulencefinder.py --help
---
> RUN cd /virulencefinder/tests && \
> python -m virulencefinder -ifa data/test.fsa -o . && \
> ls |
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Tests pass after making my changes so I'm good to merge if you are @erinyoung . Let me know and I'll merge and deploy The only other improvements I would make are to use a |
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:
Pull Request (PR) checklist:
docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15)spades/3.12.0/Dockerfile)shigatyper/2.0.1/test.sh)spades/3.12.0/README.md)