Update Ngmaster to version 1.1.1

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) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mykrobe)](https://hub.docker.com/r/staphb/mykrobe) | <details><summary> Click to see all versions </summary><ul><li>[0.11.0 (Mykrobe) & 1.9.1 (Genotyphi)](./build-files/mykrobe/0.11.0/) </li><li>[0.12.1 (Mykrobe) & 1.9.1 (Genotyphi) & 7d18a7c (sonneityping)](./build-files/mykrobe/0.12.1-sonneityping/) </li><li>[0.12.1 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping)](./build-files/mykrobe/0.12.1/) </li><li>[0.12.2 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping)](./build-files/mykrobe/0.12.2/)</li><li>[0.13.0](./build-files/mykrobe/0.13.0)</li></ul></details> | https://github.com/Mykrobe-tools/mykrobe <br/> https://github.com/typhoidgenomics/genotyphi <br/> https://github.com/katholt/sonneityping |
 | [myloasm](https://hub.docker.com/r/staphb/myloasm) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/myloasm)](https://hub.docker.com/r/staphb/myloasm) | <details><summary> Click to see all versions </summary><ul><li>[0.1.0](./build-files/myloasm/0.1.0/)</li><li>[0.2.0](./build-files/myloasm/0.2.0/)</li><li>[0.3.0](./build-files/myloasm/0.3.0/)</li></ul></details> | https://github.com/bluenote-1577/myloasm |
 | [NanoPlot](https://hub.docker.com/r/staphb/nanoplot) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/nanoplot)](https://hub.docker.com/r/staphb/nanoplot) | <details><summary> Click to see all versions </summary><ul><li>[1.27.0](./build-files/nanoplot/1.27.0/)</li><li>[1.29.0](./build-files/nanoplot/1.29.0/)</li><li>[1.30.1](./build-files/nanoplot/1.30.1/)</li><li>[1.32.0](./build-files/nanoplot/1.32.0/)</li><li>[1.33.0](./build-files/nanoplot/1.33.0/)</li><li>[1.40.0](./build-files/nanoplot/1.40.0/)</li><li>[1.41.6](./build-files/nanoplot/1.41.6/)</li><li>[1.42.0](./build-files/nanoplot/1.42.0/)</li><li>[1.46.2](./build-files/nanoplot/1.46.2/)</li></ul></details> | https://github.com/wdecoster/NanoPlot |
-| [ngmaster](https://hub.docker.com/r/staphb/ngmaster) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ngmaster)](https://hub.docker.com/r/staphb/ngmaster) | <details><summary>Click to see all versions</summary> <ul><li>[0.5.8](./build-files/ngmaster/0.5.8/)</li><li>[1.0.0](./build-files/ngmaster/1.0.0/)</li></ul> </details> | https://github.com/MDU-PHL/ngmaster |
+| [ngmaster](https://hub.docker.com/r/staphb/ngmaster) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ngmaster)](https://hub.docker.com/r/staphb/ngmaster) | <details><summary>Click to see all versions</summary> <ul><li>[0.5.8](./build-files/ngmaster/0.5.8/)</li><li>[1.0.0](./build-files/ngmaster/1.0.0/)</li><li>[1.1.1](./build-files/ngmaster/1.1.1/)</li></ul> </details> | https://github.com/MDU-PHL/ngmaster |
 | [NCBI Datasets](https://hub.docker.com/r/staphb/ncbi-datasets) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-datasets)](https://hub.docker.com/r/staphb/ncbi-datasets) | <details><summary> Click to see all versions </summary> <ul><li>[13.31.0](./build-files/ncbi-datasets/13.31.0/)</li><li>[13.35.0](./build-files/ncbi-datasets/13.35.0/)</li><li>[13.43.2](./build-files/ncbi-datasets/13.43.2/)</li><li>[14.0.0](./build-files/ncbi-datasets/14.0.0/)</li><li>[14.3.0](./build-files/ncbi-datasets/14.3.0/)</li><li>[14.7.0](./build-files/ncbi-datasets/14.7.0/)</li><li>[14.13.2](./build-files/ncbi-datasets/14.13.2/)</li><li>[14.20.0](./build-files/ncbi-datasets/14.20.0/)</li><li>[14.27.0](./build-files/ncbi-datasets/14.27.0/)</li><li>[15.1.0](./build-files/ncbi-datasets/15.1.0/)</li><li>[15.2.0](./build-files/ncbi-datasets/15.2.0/)</li><li>[15.11.0](./build-files/ncbi-datasets/15.11.0/)</li><li>[15.27.1](./build-files/ncbi-datasets/15.27.1/)</li><li>[15.31.0](./build-files/ncbi-datasets/15.31.1/)</li><li>[16.2.0](./build-files/ncbi-datasets/16.2.0/)</li><li>[16.8.1](./build-files/ncbi-datasets/16.8.1/)</li><li>[16.10.3](./build-files/ncbi-datasets/16.10.3/)</li><li>[16.15.0](./build-files/ncbi-datasets/16.15.0/)</li><li>[16.22.1](./build-files/ncbi-datasets/16.22.1/)</li><li>[16.30.0](./build-files/ncbi-datasets/16.30.0/)</li><li>[16.35.0](./build-files/ncbi-datasets/16.35.0/)</li><li>[16.38.1](./build-files/ncbi-datasets/16.38.1/)</li><li>[16.41.0](./build-files/ncbi-datasets/16.41.0/)</li><li>[18.0.2](./build-files/ncbi-datasets/18.0.2/)</li><li>[18.5.0](./build-files/ncbi-datasets/18.5.0/)</li><li>[18.7.0](./build-files/ncbi-datasets/18.7.0/)</li><li>[18.9.0](./build-files/ncbi-datasets/18.9.0/)</li><li>[18.13.0](./build-files/ncbi-datasets/18.13.0/)</li><li>[18.15.0](./build-files/ncbi-datasets/18.15.0/)</li><li>[18.17.1](./build-files/ncbi-datasets/18.17.1/)</li><li>[18.18.0](./build-files/ncbi-datasets/18.18.0/)</li></ul></details> | [https://github.com/ncbi/datasets](https://github.com/ncbi/datasets) <br/>[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) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-amrfinderplus)](https://hub.docker.com/r/staphb/ncbi-amrfinderplus) | <details><summary> Click to see all versions </summary> <ul><li>[3.1.1b](./build-files/ncbi-amrfinderplus/3.1.1b/)</li><li>[3.8.4](./build-files/ncbi-amrfinderplus/3.8.4/)</li><li>[3.8.28](./build-files/ncbi-amrfinderplus/3.8.28/)</li><li>[3.9.3](./build-files/ncbi-amrfinderplus/3.9.3/)</li><li>[3.9.8](./build-files/ncbi-amrfinderplus/3.9.8/)</li><li>[3.10.1](./build-files/ncbi-amrfinderplus/3.10.1/)</li><li>[3.10.5](./build-files/ncbi-amrfinderplus/3.10.5/)</li><li>[3.10.16](./build-files/ncbi-amrfinderplus/3.10.16/)</li><li>[3.10.20](./build-files/ncbi-amrfinderplus/3.10.20/)</li><li>[3.10.24](./build-files/ncbi-amrfinderplus/3.10.24/)</li><li>[3.10.30](./build-files/ncbi-amrfinderplus/3.10.30/)</li><li>[3.10.36](./build-files/ncbi-amrfinderplus/3.10.36)</li><li>[3.10.42](./build-files/ncbi-amrfinderplus/3.10.42/)</li><li>[3.11.2 & 2022-12-19.1](./build-files/ncbi-amrfinderplus/3.11.2/)</li><li>[3.11.2 & 2023-02-23.1](./build-file/ncbi-amrfinderplus/3.11.2-2023-02-23.1/)</li><li>[3.11.4 & 2023-02-23.1](./build-file/ncbi-amrfinderplus/3.11.4-2023-02-23.1/)</li></ul><ul><li>[3.11.8 & 2023-02-23.1](./build-files/ncbi-amrfinderplus/3.11.8-2023-02-23.1/)</li><li>[3.11.11 & 2023-04-17.1](./build-files/ncbi-amrfinderplus/3.11.11-2023-04-17.1)</li><li>[3.11.14 & 2023-04-17.1](./build-files/ncbi-amrfinderplus/3.11.14-2023-04-17.1/)</li><li>[3.11.17 & 2023-07-13.2](./build-files/ncbi-amrfinderplus/3.11.17-2023-07-13.2/)</li><li>[3.11.18 & 2023-08-08.2](./build-files/ncbi-amrfinderplus/3.11.18-2023-08-08.2/)</li><li>[3.11.20 & 2023-09-26.1](./build-files/ncbi-amrfinderplus/3.11.20-2023-09-26.1/)</li><li>[3.11.26 & 2023-11-15.1](./build-files/ncbi-amrfinderplus/3.11.26-2023-11-15.1/)</li><li>[3.12.8 & 2024-01-31.1](./build-files/ncbi-amrfinderplus/3.12.8-2024-01-31.1/)</li><li>[3.12.8 & 2024-05-02.2](./build-files/ncbi-amrfinderplus/3.12.8-2024-05-02.2/)</li><li>[3.12.8 & 2024-07-22.1](./build-files/ncbi-amrfinderplus/3.12.8-2024-07-22.1/)</li><li>[4.0.3 & 2024-10-22.1 (stxtyper now included)](./build-files/ncbi-amrfinderplus/4.0.3-2024-10-22.1/)</li><li>[4.0.3 & 2024-12-18.1](./build-files/ncbi-amrfinderplus/4.0.3-2024-12-18.1/)</li><li>[4.0.15 & 2024-12-18.1](./build-files/ncbi-amrfinderplus/4.0.15-2024-12-18.1/)</li><li>[4.0.19 & 2024-12-18.1](./build-files/ncbi-amrfinderplus/4.0.19-2024-12-18.1/)</li><li>[4.0.22 & 2025-03-25.1](./build-files/ncbi-amrfinderplus/4.0.22-2025-03-25.1/)</li><li>[4.0.23-2025-06-03.1](./build-files/ncbi-amrfinderplus/4.0.23-2025-06-03.1/)</li><li>[4.0.23-2025-07-16.1](./build-files/ncbi-amrfinderplus/4.0.23-2025-07-16.1/)</li><li>[4.2.5-2025-12-03.1](./build-files/ncbi-amrfinderplus/4.2.5-2025-12-03.1/)</li><li>[4.2.7-2026-01-21.1](./build-files/ncbi-amrfinderplus/4.2.7-2026-01-21.1/)</li></ul> </details> | [https://github.com/ncbi/amr](https://github.com/ncbi/amr) |
 | [NCBI table2asn](https://hub.docker.com/r/staphb/ncbi-table2asn) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-table2asn)](https://hub.docker.com/r/staphb/ncbi-table2asn) | <details><summary>Click to see all versions</summary> <ul><li>[1.26.678](./build-files/ncbi-table2asn/1.26.678/)</li><li>[1.28.943](./build-files/ncbi-table2asn/1.28.943/)</li><li>[1.28.1021](./build-files/ncbi-table2asn/1.28.1021/)</li><li>[1.28.1094](./build-files/ncbi-table2asn/1.28.1094/)</li><li>[1.29.1151](./build-files/ncbi-table2asn/1.29.1151/)</li><li>[1.29.324](./build-files/ncbi-table2asn/1.29.324/)</li></ul> </details> | [https://www.ncbi.nlm.nih.gov/genbank/table2asn/](https://www.ncbi.nlm.nih.gov/genbank/table2asn/) <br/>[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/) |

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

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
+```
+