adding assembly_snptyper version 0.1.1

Program_Licenses.md

@@ -13,6 +13,7 @@ The licenses of the open-source software that is contained in these Docker image
 | artic-ncov2019-epi2me | MPL 2.0 | https://github.com/epi2me-labs/wf-artic/blob/master/LICENSE |
 | any2fasta | GNU GPLv3 | https://github.com/tseemann/any2fasta/blob/master/LICENSE |
 | ARIBA | GNU GPLv3 | https://github.com/sanger-pathogens/ariba/blob/master/LICENSE |
+| assembly_snptyper | MIT | https://github.com/boasvdp/assembly_snptyper/blob/main/LICENSE |
 | Augur | GNU Affero GPLv3 | https://github.com/nextstrain/augur/blob/master/LICENSE.txt |
 | Auspice | GNU Affero GPLv3 | https://github.com/nextstrain/auspice/blob/master/LICENSE.txt |
 | Bakta | GNU GPLv3 | https://github.com/oschwengers/bakta/blob/main/LICENSE |

README.md

@@ -119,6 +119,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [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 |
 | [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 |
 | [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 |
+| [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 |
 | [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 |
 | [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 |
 | [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

@@ -0,0 +1,109 @@
+ARG ASSEMBLYSNPTYPER_VER="0.1.1"
+ARG SAMTOOLS_VER="1.19"
+ARG MINIMAP2_VER="2.28"
+
+FROM ubuntu:jammy as builder
+
+ARG SAMTOOLS_VER
+ARG MINIMAP2_VER
+
+# install dependencies required for compiling samtools
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    libncurses5-dev \
+    libbz2-dev \
+    liblzma-dev \
+    libcurl4-gnutls-dev \
+    zlib1g-dev \
+    libssl-dev \
+    gcc \
+    wget \
+    make \
+    perl \
+    bzip2 \
+    gnuplot \
+    ca-certificates \
+    curl
+
+# download, compile, and install samtools
+RUN wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VER}/samtools-${SAMTOOLS_VER}.tar.bz2 && \
+    tar -xjf samtools-${SAMTOOLS_VER}.tar.bz2 && \
+    cd samtools-${SAMTOOLS_VER} && \
+    ./configure && \
+    make && \
+    make install
+
+WORKDIR /usr/local/bin
+
+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
+
+### start of app stage ###
+FROM ubuntu:jammy as app
+
+ARG ASSEMBLYSNPTYPER_VER="0.1.1"
+
+# 'LABEL' instructions tag the image with metadata that might be important to the user
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="assembly_snptyper"
+LABEL software.version="${ASSEMBLYSNPTYPER_VER}"
+LABEL description="Type assembly based on a VCF using minimap2 + samtools"
+LABEL website="https://github.com/boasvdp/assembly_snptyper"
+LABEL license="https://github.com/boasvdp/assembly_snptyper/blob/main/LICENSE"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="[email protected]"
+
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    perl \
+    zlib1g \
+    libncurses5 \
+    bzip2 \
+    liblzma-dev \
+    libcurl4-gnutls-dev \
+    wget \
+    ca-certificates \
+    procps \
+    python3 \
+    python3-pip \
+    python-is-python3 \
+    curl \
+    unzip \
+    && apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# copy in samtools and minimap2 executables from builder stage
+COPY --from=builder /usr/local/bin/* /usr/local/bin/
+
+RUN pip install pandas
+
+# install assembly_snptyper; make /data dir
+RUN wget -q https://github.com/boasvdp/assembly_snptyper/archive/refs/tags/v${ASSEMBLYSNPTYPER_VER}.tar.gz && \
+    pip install --no-cache-dir v${ASSEMBLYSNPTYPER_VER}.tar.gz && \
+    tar -vxf v${ASSEMBLYSNPTYPER_VER}.tar.gz && \
+    mv /assembly_snptyper-${ASSEMBLYSNPTYPER_VER} /assembly_snptyper && \
+    rm v${ASSEMBLYSNPTYPER_VER}.tar.gz && \
+    mkdir /data
+
+ENV LC_ALL=C
+
+CMD [ "assembly_snptyper", "--help" ]
+
+# 'WORKDIR' sets working directory
+WORKDIR /data
+
+# A second FROM insruction creates a new stage
+FROM app as test
+
+RUN assembly_snptyper --help && \
+    assembly_snptyper --version
+
+WORKDIR /test
+
+# running on S. pyogenes representative genome
+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 && \
+    gunzip GCA_900475035.1_41965_F01_genomic.fna.gz && \
+    ls *genomic.fna > fastas.txt && \
+    assembly_snptyper --list_input fastas.txt -p 4 --reference /assembly_snptyper/data/MGAS5005.fa --vcf /assembly_snptyper/data/M1UK.vcf > m1uk.txt && \
+    head m1uk.txt
+
+RUN cd /assembly_snptyper && \
+    bash tests/test_e2e.sh

assembly_snptyper/0.1.1/README.md

@@ -0,0 +1,34 @@
+# assembly_snptyper container
+
+Main tool: [assembly_snptyper](https://github.com/boasvdp/assembly_snptyper)
+
+Code repository: https://github.com/boasvdp/assembly_snptyper
+
+Additional tools:
+- samtools: 1.19
+- minimap2: 2.28
+
+Basic information on how to use this tool:
+- executable: assembly_snptyper
+- help: -h
+- version: -v
+- description: |
+
+> 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.
+
+
+> 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.
+
+Additional information:
+
+M1UK reference and SNP vcf are located in /assembly_snptyper/data
+
+Full documentation: https://github.com/boasvdp/assembly_snptyper
+
+## Example Usage
+
+```bash
+# with a list of fasta files listed in fastas.txt
+assembly_snptyper --list_input fastas.txt -p 20 --reference /assembly_snptyper/data/MGAS5005.fa --vcf /assembly_snptyper/data/M1UK.vcf > m1uk.txt
+```
+