diff --git a/README.md b/README.md index b34e390f3..a05e48de1 100644 --- a/README.md +++ b/README.md @@ -244,7 +244,7 @@ To learn more about the docker pull rate limits and the open source software pro | [Mykrobe + Genotyphi + sonneityping](https://hub.docker.com/r/staphb/mykrobe)
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| https://github.com/Mykrobe-tools/mykrobe
https://github.com/typhoidgenomics/genotyphi
https://github.com/katholt/sonneityping | | [myloasm](https://hub.docker.com/r/staphb/myloasm)
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| https://github.com/bluenote-1577/myloasm | | [NanoPlot](https://hub.docker.com/r/staphb/nanoplot)
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| https://github.com/wdecoster/NanoPlot | -| [ngmaster](https://hub.docker.com/r/staphb/ngmaster)
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| https://github.com/MDU-PHL/ngmaster | +| [ngmaster](https://hub.docker.com/r/staphb/ngmaster)
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| https://github.com/MDU-PHL/ngmaster | | [NCBI Datasets](https://hub.docker.com/r/staphb/ncbi-datasets)
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| [https://github.com/ncbi/datasets](https://github.com/ncbi/datasets)
[https://www.ncbi.nlm.nih.gov/datasets/docs/v2/](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/) | | [NCBI AMRFinderPlus](https://hub.docker.com/r/staphb/ncbi-amrfinderplus)
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| [https://github.com/ncbi/amr](https://github.com/ncbi/amr) | | [NCBI table2asn](https://hub.docker.com/r/staphb/ncbi-table2asn)
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| [https://www.ncbi.nlm.nih.gov/genbank/table2asn/](https://www.ncbi.nlm.nih.gov/genbank/table2asn/)
[https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/](https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/) | diff --git a/build-files/ngmaster/1.1.1/Dockerfile b/build-files/ngmaster/1.1.1/Dockerfile new file mode 100644 index 000000000..95e476271 --- /dev/null +++ b/build-files/ngmaster/1.1.1/Dockerfile @@ -0,0 +1,75 @@ +FROM mambaorg/micromamba:2.5.0 AS app + +# build and run as root users since micromamba image has 'mambauser' set as the $USER +USER root +# set workdir to default for building; set to /data at the end +WORKDIR / + +# ARG sets environment variables during the build stage +ARG NGMASTER_VER="1.1.1" +ARG MLST_VER="2.23.0" +ARG ANY2FASTA_VER="0.8.1" + +LABEL base.image="mambaorg/micromamba:2.5.0" +LABEL dockerfile.version="1" +LABEL software="ngmaster" +LABEL software.version=${NGMASTER_VER} +LABEL description="In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)" +LABEL website="https://github.com/MDU-PHL/ngmaster" +LABEL license="https://github.com/MDU-PHL/ngmaster/blob/master/LICENSE" +LABEL maintainer="Curtis kapsak" +LABEL maintainer.email="curtis.kapsak@theiagen.com" + +# Install dependencies via apt-get; procps to get the 'ps' command for nextflow compatibility +# cleanup apt garbage +RUN apt-get update && apt-get install -y --no-install-recommends \ + procps && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +# install python, pip, biopython, isPcr version 33 into base micromamba env +# cleanup conda garbage +RUN micromamba install -n base -c conda-forge -c bioconda -c defaults \ + 'python>=3.7' \ + pip \ + biopython \ + any2fasta=${ANY2FASTA_VER} \ + mlst=${MLST_VER} \ + ngmaster=${NGMASTER_VER} && \ + micromamba clean -a -y + +# so that mamba/conda env is active when running below commands +ENV ENV_NAME="base" +ARG MAMBA_DOCKERFILE_ACTIVATE=1 + +# hardcode conda env into the PATH; set locale settings +ENV PATH="/opt/conda/bin:${PATH}" \ + LC_ALL=C.UTF-8 + +# set final & default working dir to /data +WORKDIR /data + +# test layer +FROM app AS test + +# so that mamba/conda env is active when running below commands +ENV ENV_NAME="base" +ARG MAMBA_DOCKERFILE_ACTIVATE=1 + +# show help and version outputs; run the program's internal tests +RUN ngmaster --help && echo && \ + ngmaster --version && mlst --version && echo && \ + ngmaster --test + +# getting unzip for unziping archive downloaded from NCBI +RUN apt-get update && apt-get install unzip curl ca-certificates -y --no-install-recommends + +# so that testing outputs are in /test +WORKDIR /test + +# test with an actual assembly downloaded from RefSeq +# more info on this genome here: https://www.ncbi.nlm.nih.gov/labs/data-hub/genome/GCF_013030075.1/ +RUN curl -OJX GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCF_013030075.1/download?include_annotation_type=GENOME_FASTA,GENOME_GFF,RNA_FASTA,CDS_FASTA,PROT_FASTA,SEQUENCE_REPORT&filename=GCF_013030075.1.zip" \ + -H "Accept: application/zip" && \ + unzip GCF_013030075.1.zip && \ + ngmaster /test/ncbi_dataset/data/GCF_013030075.1/GCF_013030075.1_ASM1303007v1_genomic.fna > ngmaster.out.tsv && \ + cat /test/ngmaster.out.tsv diff --git a/build-files/ngmaster/1.1.1/README.md b/build-files/ngmaster/1.1.1/README.md new file mode 100644 index 000000000..5b16a4905 --- /dev/null +++ b/build-files/ngmaster/1.1.1/README.md @@ -0,0 +1,24 @@ +# ngmaster 1.1.1 container + +Main tool : [ngmaster](https://github.com/MDU-PHL/ngmaster) + +In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST). + +Additional tools: + +- any2fasta 0.8.1 +- mlst 2.23.0 +- python >= 3.9.0 +- biopython 1.86 +- perl 5.32.1 +- bioperl 1.7.9 + +## Example Usage + +```bash +# test ngmaster with the test FASTA file included with ngmaster code +$ ngmaster /opt/conda/lib/python3.9/site-packages/ngmaster/test/test.fa +FILE SCHEME NG-MAST/NG-STAR porB_NG-MAST tbpB penA mtrR porB_NG-STAR ponA gyrA parC 23S +/opt/conda/lib/python3.9/site-packages/ngmaster/test/test.fa ngmaSTar 4186/231 2569 241 23 42 100 100 10 2100 +``` +