Add abricate v1.0.1 database for vibrio cholera (#963)

* add docker file, test files and database for vibrio database * fix tests * add maintainer2 * renamed database to include .fasta suffix; changed ADD to COPY as per docker reccommendation; updated test to download test FASTA instead of keeping copy in this repo; updated vibrio test commands to grep individually for expected genes * add README specific to abricate + Vcholerae DB; updated main README.md with relative links --------- Co-authored-by: kapsakcj <[email protected]>
StaPH-B · Apr 30, 2024 · f9e9da1 · f9e9da1
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diff --git a/README.md b/README.md
@@ -104,7 +104,7 @@ To learn more about the docker pull rate limits and the open source software pro
 
 | Software | Version | Link |
 | :--------: | ------- | -------- |
-| [ABRicate](https://hub.docker.com/r/staphb/abricate/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/abricate)](https://hub.docker.com/r/staphb/abricate) | <ul><li>0.8.7</li><li>0.8.13</li><li>0.8.13s (+serotypefinder db)</li><li>0.9.8</li><li>1.0.0</li><li>[1.0.1 (+ A. baumannii plasmid typing db)](https://github.com/StaPH-B/docker-builds/blob/master/abricate/1.0.1-Abaum-plasmid)</li><li>[1.0.1 (+ InsaFlu db)](https://github.com/StaPH-B/docker-builds/blob/master/abricate/1.0.1-insaflu-220727)</li></ul> | https://github.com/tseemann/abricate |
+| [ABRicate](https://hub.docker.com/r/staphb/abricate/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/abricate)](https://hub.docker.com/r/staphb/abricate) | <ul><li>0.8.7</li><li>0.8.13</li><li>0.8.13s (+serotypefinder db)</li><li>0.9.8</li><li>1.0.0</li><li>[1.0.1 (+ A. baumannii plasmid typing db)](abricate/1.0.1-Abaum-plasmid)</li><li>[1.0.1 (+ InsaFlu db)](abricate/1.0.1-insaflu-220727)</li><li>[1.0.1 (+ *Vibrio cholerae* db)](abricate/1.0.1-vibrio-cholera/)</li></ul> | https://github.com/tseemann/abricate |
 | [ACI](https://hub.docker.com/r/staphb/aci/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/aci)](https://hub.docker.com/r/staphb/aci) | <ul><li>[1.4.20240116](./aci/1.4.20240116/)</li></ul> | https://github.com/erinyoung/ACI |
 | [ANIclustermap](https://hub.docker.com/r/staphb/aniclustermap/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/aniclustermap)](https://hub.docker.com/r/staphb/aniclustermap) | <ul><li>[1.3.0](aniclusteramp/1.3.0/)</li></ul> | https://github.com/moshi4/ANIclustermap |
 | [any2fasta](https://hub.docker.com/r/staphb/any2fasta/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/any2fasta)](https://hub.docker.com/r/staphb/any2fasta) | <ul><li>0.4.2</li></ul> | https://github.com/tseemann/any2fasta |

diff --git a/abricate/1.0.1-vibrio-cholera/Dockerfile b/abricate/1.0.1-vibrio-cholera/Dockerfile
@@ -0,0 +1,121 @@
+ARG ABRICATE_VER="1.0.1"
+
+FROM ubuntu:focal as app
+
+# For easy upgrade later. ARG varibles only persist during docker image build time
+ARG ABRICATE_VER
+ARG ANY2FASTA_VERSION="0.4.2"
+
+LABEL base.image="ubuntu:focal"
+LABEL dockerfile.version="1"
+LABEL software="Abricate"
+LABEL software.version="1.0.1"
+LABEL description="Mass screening of contigs for AMR or virulence genes"
+LABEL website="https://github.com/tseemann/abricate"
+LABEL license="https://github.com/tseemann/abricate/blob/master/LICENSE"
+LABEL maintainer="Curtis Kapsak"
+LABEL maintainer.email="[email protected]"
+LABEL maintainer2="Inês Mendes"
+LABEL maintainer2.email="[email protected]"
+
+# install dependencies
+# removed: emboss
+# ncbi-blast+ version in apt for ubuntu:focal = v2.9.0 
+RUN apt-get update && apt-get install -y --no-install-recommends \
+  bioperl \
+  gzip \
+  unzip \
+  liblist-moreutils-perl \
+  libjson-perl \
+  libtext-csv-perl \
+  libfile-slurp-perl \
+  liblwp-protocol-https-perl \
+  libwww-perl \
+  libpath-tiny-perl \
+  git \
+  ncbi-blast+ \
+  wget && \
+  apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# get any2fasta
+RUN wget https://github.com/tseemann/any2fasta/archive/refs/tags/v${ANY2FASTA_VERSION}.tar.gz && \
+  tar -xvf v${ANY2FASTA_VERSION}.tar.gz && \
+  rm v${ANY2FASTA_VERSION}.tar.gz && \
+  cd any2fasta-${ANY2FASTA_VERSION} && \
+  chmod +x any2fasta && \
+  cp any2fasta /usr/local/bin
+
+# download abricate; make /data; check dependencies
+RUN wget https://github.com/tseemann/abricate/archive/v${ABRICATE_VER}.tar.gz && \
+  tar -zxvf v${ABRICATE_VER}.tar.gz && \
+  rm -rf v${ABRICATE_VER}.tar.gz && \
+  mkdir /data && \
+  /abricate-${ABRICATE_VER}/bin/abricate --check
+
+# set $PATH
+# set perl locale settings for singularity compatibility
+ENV PATH="/abricate-${ABRICATE_VER}/bin:\
+$PATH"\
+  LC_ALL=C
+
+# add custom database; rename FASTA file as 'sequences'; index database with --setupdb
+COPY vibrio_v1.0.0.fasta /
+RUN mkdir -v /abricate-${ABRICATE_VER}/db/vibrio && \
+  cp -v /vibrio_v1.0.0.fasta /abricate-${ABRICATE_VER}/db/vibrio/sequences && \
+  abricate --setupdb && \
+  abricate --list
+
+# final working directory is /data
+WORKDIR /data
+
+# testing layer starts here
+FROM app as test
+
+# Grab test Vcholerae genome, uncompress, and save to /data
+RUN wget -O - https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/018/083/565/GCA_018083565.2_PDT000793508.2/GCA_018083565.2_PDT000793508.2_genomic.fna.gz \
+  | gunzip -c > /data/GCA_018083565.2_PDT000793508.2_genomic.fna
+
+# to ensure this env variable is set in test layer
+ARG ABRICATE_VER
+
+# so that the below commands are run with /bin/bash shell and not /bin/sh - needed for bash-specific tricks below
+SHELL ["/bin/bash", "-c"]
+
+# tests shamelessly stolen and modified from: https://github.com/tseemann/abricate/blob/master/.travis.yml
+RUN set -x && \
+cd /abricate-${ABRICATE_VER}/ && \
+abricate --version && \
+abricate --help && \
+abricate --check && \
+abricate --list && \
+! abricate --doesnotexist  && \
+! abricate --threads 0 && \
+! (abricate test/assembly.fa | grep '~~~') && \
+abricate test/assembly.fa > 1.tab && \
+abricate test/assembly.fa.gz > 2.tab && \
+abricate test/assembly.gbk > 3.tab && \
+abricate test/assembly.gbk.gz > 4.tab && \
+abricate --nopath test/assembly.gbk.gz | grep '^assembly.gbk.gz' && \
+abricate --summary {1,2,3,4}.tab > summary.tab && \
+abricate --summary 1.tab 2.tab 1.tab 2>&1 | grep 'duplicate' && \
+abricate --summary <(cat 1.tab 2.tab 3.tab) | wc -l | grep -w 4 && \
+abricate test/assembly.txt |& grep ERROR && \
+abricate not_exist.embl |& grep ERROR && \
+abricate --threads `nproc` test/assembly.fa.bz2 | grep -i FOSFOMYCIN && \
+abricate --threads `nproc` test/assembly.fa.bz2 | grep -i lactam && \
+for DB in `abricate --list | cut -f1 | tail -n +2`; do abricate --db ${DB} test/assembly.fa > /dev/null ; done && \
+abricate-get_db --help && \
+abricate-get_db --db ncbi --dbdir . && \
+! grep 'FUSIDIC ACID' ncbi/sequences && \
+abricate --threads `nproc` --fofn test/fofn.txt
+
+# vibrio-specific abricate test
+# grep to find the 5 expected genes in the output TSV; error if not found
+RUN abricate --db vibrio /data/GCA_018083565.2_PDT000793508.2_genomic.fna | tee /data/abricate_vibrio.tsv && \
+  echo && \
+  echo "grepping for expected genes in abricate output now..." && \
+  grep 'ctxA' /data/abricate_vibrio.tsv && \
+  grep 'toxR' /data/abricate_vibrio.tsv && \
+  grep 'tcpA_ElTor' /data/abricate_vibrio.tsv && \
+  grep 'ompW' /data/abricate_vibrio.tsv && \
+  grep 'wbeN_O1' /data/abricate_vibrio.tsv
diff --git a/abricate/1.0.1-vibrio-cholera/README.md b/abricate/1.0.1-vibrio-cholera/README.md
@@ -0,0 +1,64 @@
+# ABRicate v1.0.1 docker image + Vibrio cholerae db
+
+> ABRicate: Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB.
+
+Main tool : [ABRicate](https://github.com/tseemann/abricate)
+
+Additional tools:
+
+- any2fasta 0.4.2
+- ncbi-blast+ 2.9.0
+- perl 5.30.0
+- bioperl 1.7.7-1
+
+## Custom *Vibrio cholerae* database info
+
+This docker image includes a *Vibrio cholerae-specific* database of gene targets (traditionally used in PCR methods) for detecting O1 & O139 serotypes, toxin-production markers, and Biotype markers within the O1 serogroup ("El Tor" or "Classical" biotypes). These sequences were shared via personal communication with Dr. Christine Lee, of the National Listeria, Yersinia, Vibrio and Enterobacterales Reference Laboratory within the Enteric Diseases Laboratory Branch at CDC.
+
+The genes included (and their purpose) included in the database are as follows:
+
+- `ctxA` - Cholera toxin, an indication of toxigenic cholerae
+- `ompW` - outer membrane protein, a *V. cholerae* species marker (presence of any allele of this gene distinguishes *V. cholerae* from *V. parahaemolyticus* and *V. vulnificus*)
+- `tcpA` - toxin co-pilus A, used to infer Biotype, either "El Tor" or "Clasical"
+  - database includes an allele for each Biotype. `tcpA_classical` and `tcpA_ElTor`
+- `toxR` - transcriptional activator (controls cholera toxin, pilus, and outer-membrane protein expression) - Species marker (allele distinguishes *V. cholerae* from *V. parahaemolyticus* and *V. vulnificus*)
+- `wbeN` - O antigen encoding region - used to identify the O1 serogroup
+- `wbfR` - O antigen encoding region - used to identify the O139 serogroup
+
+:warning: The database's FASTA file & index files are located within `/abricate-$1.0.1/db/vibrio/sequences` in the container's file system and can be utilized via the example command below.
+
+:warning: This database is identical in nucleotide sequence content to the `vibrio_230224.fasta` database included in the SRST2 container (located at `srst2/0.2.0-vibrio-230224/vibrio_230224.fasta`), but the FASTA headers were formatted for use with ABRicate.
+
+## Example Usage
+
+```bash
+# list out the available databases
+$ abricate --list
+DATABASE        SEQUENCES       DBTYPE  DATE
+card    2631    nucl    2024-Apr-30
+ncbi    5386    nucl    2024-Apr-30
+vfdb    2597    nucl    2024-Apr-30
+megares 6635    nucl    2024-Apr-30
+ecoli_vf        2701    nucl    2024-Apr-30
+argannot        2223    nucl    2024-Apr-30
+ecoh    597     nucl    2024-Apr-30
+plasmidfinder   460     nucl    2024-Apr-30
+resfinder       3077    nucl    2024-Apr-30
+vibrio  8       nucl    2024-Apr-30
+
+# run ABRicate on an Vibrio cholerae assembly using custom database, saving results to file "/data/abricate_vibrio.tsv"
+$ abricate --db vibrio /data/GCA_018083565.2_PDT000793508.2_genomic.fna | tee /data/abricate_vibrio.tsv
+abricate --nopath --db vibrio /data/GCA_018083565.2_PDT000793508.2_genomic.fna | tee /data/abricate_vibrio.tsv
+Using nucl database vibrio:  8 sequences -  2024-Apr-30
+Processing: /data/GCA_018083565.2_PDT000793508.2_genomic.fna
+#FILE   SEQUENCE        START   END     STRAND  GENE    COVERAGE        COVERAGE_MAP    GAPS    %COVERAGE       %IDENTITY       DATABASE        ACCESSION       PRODUCT RESISTANCE
+Found 5 genes in /data/GCA_018083565.2_PDT000793508.2_genomic.fna
+Tip: did you know? abricate was named after 'A'nti 'B'acterial 'R'esistiance
+Done.
+GCA_018083565.2_PDT000793508.2_genomic.fna      DADXRP020000001.1       3562    4338    +       ctxA    1-777/777       =============== 0/0     100.00  100.00  Vibriov1.0.0    CP000627.1      ctxA_O395       cholera_toxin_gene
+GCA_018083565.2_PDT000793508.2_genomic.fna      DADXRP020000001.1       520818  521702  +       toxR    1-885/885       =============== 0/0     100.00  98.42   Vibriov1.0.0    CP000627.1      toxR_O395       Vcholerae_species_marker
+GCA_018083565.2_PDT000793508.2_genomic.fna      DADXRP020000002.1       439805  440458  +       ompW    1-654/654       =============== 0/0     100.00  99.08   Vibriov1.0.0    CP000626.1      ompW_O395       Vcholerae_species_marker
+GCA_018083565.2_PDT000793508.2_genomic.fna      DADXRP020000008.1       101343  103820  +       wbeN_O1 1-2478/2478     =============== 0/0     100.00  100.00  Vibriov1.0.0    NA      wbeN_O1_INDRE   O1_serotype_marker
+GCA_018083565.2_PDT000793508.2_genomic.fna      DADXRP020000033.1       3271    3945    -       tcpA_ElTor      1-675/675       =============== 0/0     100.00  100.00  Vibriov1.0.0    CP064350.1      tcpA_ElTor_C6706        ElTor_biotype
+
+```