Merge pull request #1123 from erinyoung/erin-meningotype

adding meningotype version 0.8.5

Program_Licenses.md

@@ -105,6 +105,7 @@ The licenses of the open-source software that is contained in these Docker image
 | mashtree | GNU GPLv3 | https://github.com/lskatz/mashtree/blob/master/LICENSE |
 | MaSuRCA | GNU GPLv3 | https://github.com/alekseyzimin/masurca/blob/master/LICENSE.txt
 | Medaka | Mozilla Public License 2.0 | https://github.com/nanoporetech/medaka/blob/master/LICENSE.md |
+| meningotype | GNU General Public License v3.0 | https://github.com/MDU-PHL/meningotype/blob/master/LICENSE |
 | Metaphlan | MIT | https://github.com/biobakery/MetaPhlAn/blob/master/license.txt |
 | MIDAS | GNU GPLv3 |https://github.com/snayfach/MIDAS/blob/master/LICENSE |
 | minimap2 | MIT | https://github.com/lh3/minimap2/blob/master/LICENSE.txt |

README.md

@@ -214,6 +214,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [mashtree](https://hub.docker.com/r/staphb/mashtree) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mashtree)](https://hub.docker.com/r/staphb/mashtree) | <ul><li>[0.52.0](./mashtree/0.52.0/)</li><li>[0.57.0](./mashtree/0.57.0/)</li><li>[1.0.4](./mashtree/1.0.4/)</li><li>[1.2.0](./mashtree/1.2.0/)</li><li>[1.4.6](./mashtree/1.4.6/)</li></ul> | https://github.com/lskatz/mashtree |
 | [MaSuRCA](https://hub.docker.com/r/staphb/masurca) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/masurca)](https://hub.docker.com/r/staphb/masurca) | <ul><li>4.0.8</li><li>4.0.9</li><li>4.1.0</li></ul> | https://github.com/alekseyzimin/masurca |
 | [medaka](https://hub.docker.com/r/staphb/medaka) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/medaka)](https://hub.docker.com/r/staphb/medaka) | <ul><li>[0.8.1](./medaka/0.8.1/)</li><li>[1.0.1](./medaka/1.0.1/)</li><li>[1.2.0](./medaka/1.2.0/)</li><li>[2.0.0](./medaka/2.0.0/)</li><li>[2.0.1](./medaka/2.0.1/)</li></ul> | https://github.com/nanoporetech/medaka |
+| [meningotype](https://hub.docker.com/r/staphb/meningotype) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/meningotype)](https://hub.docker.com/r/staphb/meningotype) | <ul><li>[0.8.5](./meningotype/0.8.5/)</li></ul> | https://github.com/MDU-PHL/meningotype |
 | [metaphlan](https://hub.docker.com/r/staphb/metaphlan) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/metaphlan)](https://hub.docker.com/r/staphb/metaphlan) | <ul><li>[3.0.3-no-db (no database)](./metaphlan/3.0.3-no-db/)</li><li> [3.0.3 (~3GB db)](./metaphlan/3.0.3/)</li><li>[4.1.0](./metaphlan/4.1.0/) (no database)</li><li>[4.1.1](./metaphlan/4.1.1/) (no database)</li></ul> | https://github.com/biobakery/MetaPhlAn |
 | [MIDAS](https://hub.docker.com/r/staphb/midas) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/midas)](https://hub.docker.com/r/staphb/midas) | <ul><li>1.3.2 (no database)</li> | https://github.com/snayfach/MIDAS |
 | [minimap2](https://hub.docker.com/r/staphb/minimap2) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/minimap2)](https://hub.docker.com/r/staphb/minimap2) | <ul><li>2.17</li><li>2.18</li><li>2.21</li><li>2.22</li><li>2.23</li><li>2.24</li><li>2.25</li><li>[2.26](./minimap2/2.26)</li><li>[2.27](./minimap2/2.27/)</li><li>[2.28](./minimap2/2.28/)</li></ul> | https://github.com/lh3/minimap2 |

meningotype/0.8.5/Dockerfile

@@ -0,0 +1,116 @@
+ARG MENINGOTYPE_VER="0.8.5"
+ARG ISPCR_VER="33"
+ARG MLST_VER="2.23.0"
+ARG ANY2FASTA_VER="0.4.2"
+
+## Builder ##
+FROM ubuntu:jammy AS builder
+
+ARG ISPCR_VER
+ARG MACHTYPE="x86_64-pc-linux-gnu"
+
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    wget \
+    unzip
+
+RUN wget https://hgwdev.gi.ucsc.edu/~kent/src/isPcr${ISPCR_VER}.zip &&\
+    unzip isPcr${ISPCR_VER}.zip &&\
+    cd isPcrSrc &&\
+    sed -i 's/-Werror//g' inc/common.mk &&\
+    mkdir -p bin/$MACHTYPE &&\
+    mkdir -p lib/$MACHTYPE &&\
+    make HOME=$PWD MACHTYPE=${MACHTYPE} C_INCLUDE_PATH=/usr/include LIBRARY_PATH=/usr/lib CFLAGS="-fcommon" &&\
+    mv bin/$MACHTYPE/* /usr/local/bin/
+
+## App ##
+FROM ubuntu:jammy AS app
+
+ARG MENINGOTYPE_VER
+ARG MLST_VER
+ARG ANY2FASTA_VER
+
+# 'LABEL' instructions tag the image with metadata that might be important to the user
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="meningotype"
+LABEL software.version="${MENINGOTYPE_VER}"
+LABEL description="In silico typing of Neisseria meningitidis"
+LABEL website="https://github.com/MDU-PHL/meningotype"
+LABEL license="https://github.com/MDU-PHL/meningotype?tab=GPL-3.0-1-ov-file#readme"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="eriny@utah.gov"
+
+# most of these dependencies are for mlst
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    libmoo-perl \
+    liblist-moreutils-perl \
+    libjson-perl \
+    gzip \
+    file \
+    ncbi-blast+ \
+    libfile-which-perl \
+    curl \
+    parallel \
+    procps \
+    python3 \
+    python3-pip && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+COPY --from=builder /usr/local/bin/* /usr/local/bin/
+
+# get any2fasta; move binary to /usr/local/bin which is already in $PATH
+RUN wget -q https://github.com/tseemann/any2fasta/archive/refs/tags/v${ANY2FASTA_VER}.tar.gz && \
+    tar xzf v${ANY2FASTA_VER}.tar.gz && \
+    rm v${ANY2FASTA_VER}.tar.gz && \
+    chmod +x any2fasta-${ANY2FASTA_VER}/any2fasta && \
+    mv -v any2fasta-${ANY2FASTA_VER}/any2fasta /usr/local/bin && \
+    rm -rf any2fasta-${ANY2FASTA_VER}
+
+# get mlst
+RUN wget -q https://github.com/tseemann/mlst/archive/v${MLST_VER}.tar.gz && \
+    tar -xzf v${MLST_VER}.tar.gz && \
+    rm -v v${MLST_VER}.tar.gz
+
+# get meningotype
+RUN wget -q https://github.com/MDU-PHL/meningotype/archive/refs/tags/v${MENINGOTYPE_VER}.tar.gz && \
+    pip install --no-cache-dir v${MENINGOTYPE_VER}.tar.gz && \
+    rm -rf v${MENINGOTYPE_VER}.tar.gz && \
+    meningotype -h
+
+# set PATH and perl local settings
+ENV PATH="${PATH}:/mlst-${MLST_VER}/bin:" \
+    LC_ALL=C.UTF-8
+
+# update the database
+RUN meningotype --updatedb
+
+# 'CMD' instructions set a default command when the container is run. This is typically 'tool --help.'
+CMD [ "meningotype", "--help" ]
+
+# 'WORKDIR' sets working directory
+WORKDIR /data
+
+## Test ##
+FROM app AS test
+
+# set working directory so that all test inputs & outputs are kept in /test
+WORKDIR /test
+
+# print help and version info; check dependencies (not all software has these options available)
+# Mostly this ensures the tool of choice is in path and is executable
+RUN meningotype --help && \
+    meningotype --version 
+
+# Run the program's internal tests if available
+RUN meningotype --test && \
+    meningotype --test --finetype && \
+    meningotype --test --all
+
+# Option 2: write below common usage cases
+RUN wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/022/869/645/GCA_022869645.1_ASM2286964v1/GCA_022869645.1_ASM2286964v1_genomic.fna.gz && \
+    gzip -d GCA_022869645.1_ASM2286964v1_genomic.fna.gz && \
+    meningotype GCA_022869645.1_ASM2286964v1_genomic.fna > results.txt && \
+    head results.txt

meningotype/0.8.5/README.md

@@ -0,0 +1,27 @@
+# meningotype container
+
+Main tool: [meningotype](https://github.com/MDU-PHL/meningotype)
+
+Code repository: https://github.com/MDU-PHL/meningotype
+
+Additional tools:
+- blast: 2.12.0+
+- isPCR: 33
+- mlst: 2.23.0
+- any2fasta: 0.4.2
+
+Basic information on how to use this tool:
+- executable: meningotype
+- help: --help
+- version: --version
+- description: In silico typing for Neisseria meningitidis
+
+Additional information: Documentation sometimes shows `meningotype.py` usage, but this is not in PATH. Please use `meningotype`.
+
+Full documentation: https://github.com/MDU-PHL/meningotype
+
+## Example Usage
+
+```bash
+meningotype --finetype *fasta > results.txt
+```