Update Ngmaster to version 1.1.1

[cwoodside1278]

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/build-files/samtools/1.15 )
• Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number in build-files (i.e. docker-builds/build-files/spades/3.12.0/Dockerfile)
  • (optional) All test files are located in same directory as the Dockerfile (i.e. build-files/shigatyper/2.0.1/test.sh)
• Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. docker-builds/build-files/spades/3.12.0/README.md)
  • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
• Dockerfile includes the recommended LABELS
• Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

Description

Updated ngmaster to 1.1.1 version from 1.0.0

• created new directory structure ngmaster/1.1.1
• Updated the micromamba to a much newer version: 'FROM mambaorg/micromamba:2.5.0 AS app_base'
• Updated any2fasta version to 0.8.1
• Updated the container-specific read me to ngmaster/1.1.1
• Updated the main read me to include the new version

Diff Output

diff -r ngmaster/1.1.1/Dockerfile ngmaster/1.0.0/Dockerfile
1c1
< FROM mambaorg/micromamba:2.5.0 AS app
---
> FROM mambaorg/micromamba:1.3.0 as app
9c9
< ARG NGMASTER_VER="1.1.1"
---
> ARG NGMASTER_VER="1.0.0"
11c11
< ARG ANY2FASTA_VER="0.8.1"
---
> ARG ANY2FASTA_VER="0.4.2"
13,14c13,14
< LABEL base.image="mambaorg/micromamba:2.5.0"
< LABEL dockerfile.version="1"
---
> LABEL base.image="mambaorg/micromamba:1.3.0"
> LABEL dockerfile.version="2"
52c52
< FROM app AS test
---
> FROM app as test
75c75
<  cat /test/ngmaster.out.tsv
---
>  cat /test/ngmaster.out.tsv
\ No newline at end of file
diff -r ngmaster/1.1.1/README.md ngmaster/1.0.0/README.md
1,24c1,23
< # 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
< ```
< 
---
> # ngmaster 1.0.0 container
> 
> Main tool : [ngmaster](https://github.com/MDU-PHL/ngmaster)
> 
> In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST).
> 
> Additional tools:
> 
> - any2fasta 0.4.2
> - mlst 2.23.0
> - python 3.9.0
> - biopython 1.80
> - 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
> ```

Test Build

[+] Building 0.6s (12/12) FINISHED                                                                                                                                    docker:default
 => [internal] load build definition from Dockerfile                                                                                                                            0.0s
 => => transferring dockerfile: 2.79kB                                                                                                                                          0.0s
 => [internal] load metadata for docker.io/mambaorg/micromamba:2.5.0                                                                                                            0.3s
 => [internal] load .dockerignore                                                                                                                                               0.0s
 => => transferring context: 2B                                                                                                                                                 0.0s
 => [app 1/5] FROM docker.io/mambaorg/micromamba:2.5.0@sha256:af06736ba66714dd4b18b63011e4405091561b8777da14da30ba618ef280c0b5                                                  0.0s
 => => resolve docker.io/mambaorg/micromamba:2.5.0@sha256:af06736ba66714dd4b18b63011e4405091561b8777da14da30ba618ef280c0b5                                                      0.0s
 => CACHED [app 2/5] RUN apt-get update && apt-get install -y --no-install-recommends  procps &&  apt-get autoclean && rm -rf /var/lib/apt/lists/*                              0.0s
 => CACHED [app 3/5] RUN micromamba install -n base -c conda-forge -c bioconda -c defaults  'python>=3.7'  pip  biopython  any2fasta=0.8.1  mlst=2.23.0  ngmaster=1.1.1 &&  mi  0.0s
 => CACHED [app 4/5] WORKDIR /data                                                                                                                                              0.0s
 => CACHED [test 1/4] RUN ngmaster --help && echo &&  ngmaster --version && mlst --version && echo &&  ngmaster --test                                                          0.0s
 => CACHED [test 2/4] RUN apt-get update && apt-get install unzip curl ca-certificates -y --no-install-recommends                                                               0.0s
 => CACHED [test 3/4] WORKDIR /test                                                                                                                                             0.0s
 => CACHED [test 4/4] RUN curl -OJX GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCF_013030075.1/download?include_annotation_type=GENOME_FASTA,GENOME_G  0.0s
 => exporting to image                                                                                                                                                          0.1s
 => => exporting layers                                                                                                                                                         0.0s
 => => exporting manifest sha256:2279483e9a73f492c77a9d11380d769c82778e3cb1baa444ad5f1852858d3fc6                                                                               0.0s
 => => exporting config sha256:c04bdcc73968f3ea8ecb80bedb627a18a1953bfdad8ad01aeda665e80d57fcbb                                                                                 0.0s
 => => exporting attestation manifest sha256:a30b7f812d42379d084cf20e62888bca777f92fd3e359fe71923ffcb0138701b                                                                   0.0s
 => => exporting manifest list sha256:d314d13d0cc798e47afcd4bd89311f8a40d84dbeab9e79400571ea3d55c351d4                                                                          0.0s
 => => naming to docker.io/library/ngmaster:1.1.1                                                                                                                               0.0s
 => => unpacking to docker.io/library/ngmaster:1.1.1              

[erinyoung]

Tests worked

#12 [test 4/4] 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
#12 0.081   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
#12 0.081                                  Dload  Upload   Total   Spent    Left  Speed
#12 0.081 
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 57008    0 57008    0     0  84870      0 --:--:-- --:--:-- --:--:-- 84833
100 1843k    0 1843k    0     0  1712k      0 --:--:--  0:00:01 --:--:-- 1713k
#12 1.162 Archive:  GCF_013030075.1.zip
#12 1.162   inflating: README.md               
#12 1.162   inflating: ncbi_dataset/data/assembly_data_report.jsonl  
#12 1.162   inflating: ncbi_dataset/data/GCF_013030075.1/cds_from_genomic.fna  
#12 1.178   inflating: ncbi_dataset/data/GCF_013030075.1/GCF_013030075.1_ASM1303007v1_genomic.fna  
#12 1.192   inflating: ncbi_dataset/data/GCF_013030075.1/genomic.gff  
#12 1.200   inflating: ncbi_dataset/data/GCF_013030075.1/protein.faa  
#12 1.207   inflating: ncbi_dataset/data/GCF_013030075.1/sequence_report.jsonl  
#12 1.207   inflating: ncbi_dataset/data/dataset_catalog.json  
#12 1.207   inflating: md5sum.txt              
#12 7.131 FILE	SCHEME	NG-MAST/NG-STAR	porB_NG-MAST	tbpB	penA	mtrR	porB_NG-STAR	ponA	gyrA	parC	23S
#12 7.131 /test/ncbi_dataset/data/GCF_013030075.1/GCF_013030075.1_ASM1303007v1_genomic.fna	ngmaSTar	4093/-	2488	10	1691?	19	11	-	5	2	100,100,100,100
#12 DONE 7.1s

[erinyoung]

I have no changes to recommend. Thank you for putting this together.

[erinyoung]

Thank you for putting this together! You can check the status of the deploy here : https://github.com/StaPH-B/docker-builds/actions/runs/23012998889