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adding assembly_snptyper version 0.1.1 (#1016)
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‎Program_Licenses.md‎

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| artic-ncov2019-epi2me | MPL 2.0 | https://github.com/epi2me-labs/wf-artic/blob/master/LICENSE |
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| any2fasta | GNU GPLv3 | https://github.com/tseemann/any2fasta/blob/master/LICENSE |
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| ARIBA | GNU GPLv3 | https://github.com/sanger-pathogens/ariba/blob/master/LICENSE |
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| assembly_snptyper | MIT | https://github.com/boasvdp/assembly_snptyper/blob/main/LICENSE |
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| Augur | GNU Affero GPLv3 | https://github.com/nextstrain/augur/blob/master/LICENSE.txt |
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| Auspice | GNU Affero GPLv3 | https://github.com/nextstrain/auspice/blob/master/LICENSE.txt |
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| Bakta | GNU GPLv3 | https://github.com/oschwengers/bakta/blob/main/LICENSE |

‎README.md‎

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| [artic-ncov2019-epi2me](https://hub.docker.com/r/staphb/artic-ncov2019-epi2me) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/artic-ncov2019-epi2me)](https://hub.docker.com/r/staphb/artic-ncov2019-epi2me) | <ul><li>0.3.10</ul> | https://github.com/epi2me-labs/wf-artic |
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| [artic-ncov2019-medaka](https://hub.docker.com/r/staphb/artic-ncov2019-medaka) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/artic-ncov2019-medaka)](https://hub.docker.com/r/staphb/artic-ncov2019-medaka) | <ul><li>1.1.0</ul> | https://github.com/artic-network/artic-ncov2019 |
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| [artic-ncov2019-nanopolish](https://hub.docker.com/r/staphb/artic-ncov2019-nanopolish) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/artic-ncov2019-nanopolish)](https://hub.docker.com/r/staphb/artic-ncov2019-nanopolish) | <ul><li>1.1.0</ul> | https://github.com/artic-network/artic-ncov2019 |
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| [assembly_snptyper](https://hub.docker.com/r/staphb/assembly_snptyperh) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/assembly_snptyper)](https://hub.docker.com/r/staphb/assembly_snptyper) | <ul><li>[0.1.1](./assembly_snptyper/0.1.1/)</li></ul> | https://github.com/boasvdp/assembly_snptyper |
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| [Augur](https://hub.docker.com/r/staphb/augur) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/augur)](https://hub.docker.com/r/staphb/augur) | <ul><li>[6.3.0](./augur/6.3.0/)</li><li>[7.0.2](./augur/7.0.2/)</li><li>[8.0.0](./augur/8.0.0/)</li><li>[9.0.0](./augur/9.0.0/)</li><li>[16.0.3](./augur/16.0.3/)</li><li>[24.2.2](./augur/24.2.2/)</li><li>[24.2.3](./augur/24.2.3/)</li><li>[24.3.0](./augur/24.3.0/)</li><li>[24.4.0](./augur/24.4.0/)</li></ul> | https://github.com/nextstrain/augur |
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| [Auspice](https://hub.docker.com/r/staphb/auspice) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/auspice)](https://hub.docker.com/r/staphb/auspice) | <ul><li>2.12.0</li></ul> | https://github.com/nextstrain/auspice |
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| [bakta](https://hub.docker.com/r/staphb/bakta) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bakta)](https://hub.docker.com/r/staphb/bakta) | <ul><li>[1.9.2](./bakta/1.9.2/)</li><li>[1.9.2-light](./bakta/1.9.2-5.1-light/)</li><li>[1.9.3](./bakta/1.9.3/)</li><li>[1.9.3-light](./bakta/1.9.3-5.1-light/)</li><li>[1.9.4](./bakta/1.9.4/)</li></ul> | https://github.com/oschwengers/bakta |

‎assembly_snptyper/0.1.1/Dockerfile‎

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ARG ASSEMBLYSNPTYPER_VER="0.1.1"
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ARG SAMTOOLS_VER="1.19"
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ARG MINIMAP2_VER="2.28"
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FROM ubuntu:jammy as builder
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ARG SAMTOOLS_VER
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ARG MINIMAP2_VER
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# install dependencies required for compiling samtools
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RUN apt-get update && apt-get install --no-install-recommends -y \
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libncurses5-dev \
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libbz2-dev \
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liblzma-dev \
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libcurl4-gnutls-dev \
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zlib1g-dev \
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libssl-dev \
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gcc \
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wget \
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make \
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perl \
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bzip2 \
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gnuplot \
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ca-certificates \
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curl
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# download, compile, and install samtools
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RUN wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VER}/samtools-${SAMTOOLS_VER}.tar.bz2 && \
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tar -xjf samtools-${SAMTOOLS_VER}.tar.bz2 && \
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cd samtools-${SAMTOOLS_VER} && \
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./configure && \
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make && \
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make install
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WORKDIR /usr/local/bin
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RUN curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VER}/minimap2-${MINIMAP2_VER}_x64-linux.tar.bz2 | tar -jxvf - --no-same-owner
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### start of app stage ###
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FROM ubuntu:jammy as app
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ARG ASSEMBLYSNPTYPER_VER="0.1.1"
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# 'LABEL' instructions tag the image with metadata that might be important to the user
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LABEL base.image="ubuntu:jammy"
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LABEL dockerfile.version="1"
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LABEL software="assembly_snptyper"
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LABEL software.version="${ASSEMBLYSNPTYPER_VER}"
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LABEL description="Type assembly based on a VCF using minimap2 + samtools"
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LABEL website="https://github.com/boasvdp/assembly_snptyper"
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LABEL license="https://github.com/boasvdp/assembly_snptyper/blob/main/LICENSE"
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LABEL maintainer="Erin Young"
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LABEL maintainer.email="eriny@utah.gov"
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ARG DEBIAN_FRONTEND=noninteractive
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RUN apt-get update && apt-get install --no-install-recommends -y \
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perl \
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zlib1g \
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libncurses5 \
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bzip2 \
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liblzma-dev \
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libcurl4-gnutls-dev \
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wget \
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ca-certificates \
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procps \
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python3 \
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python3-pip \
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python-is-python3 \
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curl \
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unzip \
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&& apt-get autoclean && rm -rf /var/lib/apt/lists/*
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# copy in samtools and minimap2 executables from builder stage
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COPY --from=builder /usr/local/bin/* /usr/local/bin/
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RUN pip install pandas
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# install assembly_snptyper; make /data dir
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RUN wget -q https://github.com/boasvdp/assembly_snptyper/archive/refs/tags/v${ASSEMBLYSNPTYPER_VER}.tar.gz && \
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pip install --no-cache-dir v${ASSEMBLYSNPTYPER_VER}.tar.gz && \
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tar -vxf v${ASSEMBLYSNPTYPER_VER}.tar.gz && \
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mv /assembly_snptyper-${ASSEMBLYSNPTYPER_VER} /assembly_snptyper && \
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rm v${ASSEMBLYSNPTYPER_VER}.tar.gz && \
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mkdir /data
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ENV LC_ALL=C
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CMD [ "assembly_snptyper", "--help" ]
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# 'WORKDIR' sets working directory
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WORKDIR /data
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# A second FROM insruction creates a new stage
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FROM app as test
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RUN assembly_snptyper --help && \
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assembly_snptyper --version
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WORKDIR /test
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# running on S. pyogenes representative genome
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RUN wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/475/035/GCA_900475035.1_41965_F01/GCA_900475035.1_41965_F01_genomic.fna.gz && \
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gunzip GCA_900475035.1_41965_F01_genomic.fna.gz && \
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ls *genomic.fna > fastas.txt && \
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assembly_snptyper --list_input fastas.txt -p 4 --reference /assembly_snptyper/data/MGAS5005.fa --vcf /assembly_snptyper/data/M1UK.vcf > m1uk.txt && \
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head m1uk.txt
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RUN cd /assembly_snptyper && \
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bash tests/test_e2e.sh

‎assembly_snptyper/0.1.1/README.md‎

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# assembly_snptyper container
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Main tool: [assembly_snptyper](https://github.com/boasvdp/assembly_snptyper)
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Code repository: https://github.com/boasvdp/assembly_snptyper
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Additional tools:
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- samtools: 1.19
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- minimap2: 2.28
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Basic information on how to use this tool:
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- executable: assembly_snptyper
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- help: -h
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- version: -v
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- description: |
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> This software can take a bacterial genome assembly in fasta format, align it to a reference genome and search for specific SNPs based on the alignment. It uses minimap2 and samtools to do this. You would typically only run this tool instead of a read mapping tool if you don't have access to the sequence reads.
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> The tool was written with M1UK typing in mind. In this specific case, the reference genome is an M1global strain, from which M1UK can be discerned by only 27 lineage-specific SNPs. Important assumptions here are that the type of interest (here, M1UK) is closely related to the reference genome, warranting the use of the asm5 preset for minimap2.
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Additional information:
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M1UK reference and SNP vcf are located in /assembly_snptyper/data
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Full documentation: https://github.com/boasvdp/assembly_snptyper
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## Example Usage
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```bash
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# with a list of fasta files listed in fastas.txt
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assembly_snptyper --list_input fastas.txt -p 20 --reference /assembly_snptyper/data/MGAS5005.fa --vcf /assembly_snptyper/data/M1UK.vcf > m1uk.txt
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```
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