diff --git a/ncbi-amrfinderplus/3.11.4-2023-02-23.1/Dockerfile b/ncbi-amrfinderplus/3.11.4-2023-02-23.1/Dockerfile
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-FROM ubuntu:jammy as app
-
-ARG AMRFINDER_VER="3.11.4"
-ARG AMRFINDER_DB_VER="2023-02-23.1"
-
-LABEL base.image="ubuntu:jammy"
-LABEL dockerfile.version="1"
-LABEL software="NCBI AMRFinderPlus"
-LABEL software.version="${AMRFINDER_VER}"
-LABEL description="NCBI resistance gene detection tool"
-LABEL website="https://github.com/ncbi/amr"
-LABEL license="https://github.com/ncbi/amr/blob/master/LICENSE"
-LABEL maintainer="Kelsey Florek"
-LABEL maintainer.email="kelsey.florek@slh.wisc.edu"
-LABEL maintainer2="Curtis Kapsak"
-LABEL maintainer2.email="kapsakcj@gmail.com"
-LABEL maintainer3="Anders Goncalves da Silva"
-LABEL maintainer3.email="andersgs@gmail.com"
-LABEL maintainer4="Erin Young"
-LABEL maintainer4.email="eriny@utah.gov"
-LABEL maintainer5="Holly McQueary"
-LABEL maintainer5.email="holly.c.mcqueary@mass.gov"
-
-# ncbi-blast+ installed via apt is v2.12.0
-# hmmer installed via apt is v3.3.2
-RUN apt-get update && apt-get install -y --no-install-recommends \
- ca-certificates \
- wget \ 
- curl \
- make \
- g++ \
- ncbi-blast+ \
- hmmer \
- procps && \
- apt-get autoclean && \
- rm -rf /var/lib/apt/lists/*
-
-# download and install amrfinderplus pre-compiled binaries; make /data
-RUN mkdir amrfinder && cd /amrfinder && \
- wget https://github.com/ncbi/amr/releases/download/amrfinder_v${AMRFINDER_VER}/amrfinder_binaries_v${AMRFINDER_VER}.tar.gz && \
- tar zxf amrfinder_binaries_v${AMRFINDER_VER}.tar.gz && \
- rm amrfinder_binaries_v${AMRFINDER_VER}.tar.gz && \
- mkdir /data
-
-# set PATH and locale settings for singularity compatibiliity
-ENV PATH="${PATH}:\
-/amrfinder"\
- LC_ALL=C
-
-# download databases and index them
-# done in this manner to pin the database version instead of pulling the latest version with `amrfinder -u` 
-# softlink is required for `amrfinder -l` and typical `amrfinder` use cases to work properly
-RUN mkdir -p /amrfinder/data/${AMRFINDER_DB_VER} && \
-wget -q -P /amrfinder/data/${AMRFINDER_DB_VER} ftp://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/3.11/${AMRFINDER_DB_VER}/* && \
-amrfinder_index /amrfinder/data/${AMRFINDER_DB_VER} && \
-ln -s /amrfinder/data/${AMRFINDER_DB_VER} /amrfinder/data/latest
-
-# set final working directory
-WORKDIR /data
-
-# default command is to print help options
-CMD [ "amrfinder", "--help" ]
-
-## Test stage
-FROM app as test
-
-# list database version and available --organism options
-RUN amrfinder -l
-
-# run recommended tests from amrfinder
-RUN amrfinder --plus -p /amrfinder/test_prot.fa -g  /amrfinder/test_prot.gff -O Escherichia > test_prot.got && \
-  diff /amrfinder/test_prot.expected test_prot.got && \
-  amrfinder --plus -n /amrfinder/test_dna.fa -O Escherichia > test_dna.got && \
-  diff /amrfinder/test_dna.expected test_dna.got && \
-  amrfinder --plus -n /amrfinder/test_dna.fa -p /amrfinder/test_prot.fa -g /amrfinder/test_prot.gff -O Escherichia > test_both.got && \
-  diff /amrfinder/test_both.expected test_both.got
-
-# run amrfinder on Salmonella, without and with --organism option
-RUN wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/010/941/835/GCA_010941835.1_PDT000052640.3/GCA_010941835.1_PDT000052640.3_genomic.fna.gz  && \
-  gzip -d GCA_010941835.1_PDT000052640.3_genomic.fna.gz && \
-  amrfinder --plus --nucleotide GCA_010941835.1_PDT000052640.3_genomic.fna --output test1.txt && \
-  amrfinder --plus --nucleotide GCA_010941835.1_PDT000052640.3_genomic.fna --organism Salmonella --output test2.txt && \
-  cat test1.txt test2.txt
-
-# run amrfinder on Klebesiella oxytoca using --organism/-O flag
-RUN wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/812/925/GCA_003812925.1_ASM381292v1/GCA_003812925.1_ASM381292v1_genomic.fna.gz && \
-  gzip -d GCA_003812925.1_ASM381292v1_genomic.fna.gz && \
-  amrfinder --plus --name GCA_003812925.1 -n GCA_003812925.1_ASM381292v1_genomic.fna  -O Klebsiella_oxytoca -o GCA_003812925.1-amrfinder.tsv