Ariba version 2.14.7

README.md

@@ -107,7 +107,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [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 |
 | [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 |
-| [ARIBA](https://hub.docker.com/r/staphb/ariba/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ariba)](https://hub.docker.com/r/staphb/ariba) | <ul><li>2.14.4</li><li>[2.14.6](ariba/2.14.6/)</li></ul> | https://github.com/sanger-pathogens/ariba |
+| [ARIBA](https://hub.docker.com/r/staphb/ariba/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ariba)](https://hub.docker.com/r/staphb/ariba) | <ul><li>[2.14.4](./ariba/2.14.4/)</li><li>[2.14.6](./ariba/2.14.6/)</li><li>[2.14.7](./ariba/2.14.7/)</li></ul> | https://github.com/sanger-pathogens/ariba |
 | [artic](https://hub.docker.com/r/staphb/artic) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/artic)](https://hub.docker.com/r/staphb/artic) | <ul><li>[1.2.4-1.11.1 (artic-medaka)](artic/1.2.4-1.11.1/)</ul> | https://github.com/artic-network/fieldbioinformatics |
 | [artic-ncov2019](https://hub.docker.com/r/staphb/artic-ncov2019) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/artic-ncov2019)](https://hub.docker.com/r/staphb/artic-ncov2019) | <ul><li>1.3.0</ul> | https://github.com/artic-network/fieldbioinformatics |
 | [artic-ncov2019-epi2me](https://hub.docker.com/r/staphb/artic-ncov2019-epi2me) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/artic-ncov2019-epi2me)](https://hub.docker.com/r/staphb/artic-ncov2019-epi2me) | <ul><li>0.3.10</ul> | https://github.com/epi2me-labs/wf-artic |

ariba/2.14.7/Dockerfile

@@ -0,0 +1,92 @@
+FROM ubuntu:jammy as app
+
+# for easy upgrade later. ARG variables only persist during build time
+ARG ARIBA_VER="2.14.7"
+
+# versions from https://github.com/sanger-pathogens/ariba/blob/71909ed5b068723119e941045d25ed60328e70e7/install_dependencies.sh
+ARG SPADES_VER="3.13.1"
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="ARIBA"
+LABEL software.version="${ARIBA_VER}"
+LABEL description="ARIBA: Antimicrobial Resistance Identification By Assembly"
+LABEL website="https://github.com/sanger-pathogens/ariba"
+LABEL license="https://github.com/sanger-pathogens/ariba/blob/master/LICENSE"
+LABEL maintainer="Curtis Kapsak"
+LABEL maintainer.email="[email protected]"
+LABEL maintainer2="Harry Hung"
+LABEL maintainer2.email="[email protected]"
+
+# prevents having to enter commands during apt-get install
+ARG DEBIAN_FRONTEND=noninteractive
+
+# dependencies
+RUN apt-get update && apt-get install --no-install-recommends -y \
+  python3-dev \
+  python3-pip \
+  python3-tk \
+  python3-setuptools \
+  python3-wheel \
+  cython3 \
+  zlib1g-dev \
+  bowtie2 \
+  mummer \
+  cd-hit \
+  wget \
+  curl \
+  gawk \
+  locales-all \
+  build-essential \
+  libbz2-dev \
+  libjpeg-dev  \
+  liblzma-dev  \
+  autoconf \
+  automake \
+  perl \
+  libcurl4-gnutls-dev \
+  libssl-dev \
+  libncurses5 && \
+  apt-get autoclean && rm -rf /var/lib/apt/lists/* 
+
+ENV LANG=en_US.UTF-8 \
+    LANGUAGE=en_US:en 
+
+# optional installation to enable the usage of SPAdes assembler
+RUN wget -q https://github.com/ablab/spades/releases/download/v${SPADES_VER}/SPAdes-${SPADES_VER}-Linux.tar.gz && \
+  tar -xzf SPAdes-${SPADES_VER}-Linux.tar.gz && \
+  rm SPAdes-${SPADES_VER}-Linux.tar.gz
+
+# needed to avoid a matplotlib error
+# https://github.com/sanger-pathogens/ariba/blob/b1b524c9d9588cba9d998c9121bd74c63856526/Dockerfile#L49
+ENV MPLBACKEND="agg"
+
+# install ariba with pip3
+RUN wget -q https://github.com/sanger-pathogens/ariba/archive/refs/tags/v${ARIBA_VER}.tar.gz && \
+  pip3 install v${ARIBA_VER}.tar.gz && \
+  rm -rf v${ARIBA_VER}.tar.gz && \
+  mkdir /data
+
+# set $PATH and locale settings for singularity compatibility
+ENV PATH="/SPAdes-${SPADES_VER}-Linux/bin:$PATH" \
+  LC_ALL=C
+
+WORKDIR /data
+
+# default command is to pull up help options
+CMD ["ariba", "--help"]
+
+# new base for testing
+FROM app as test
+
+# print out ARIBA version and 
+RUN ariba version
+
+# run built-in test and confirm files are successfully created
+RUN ariba test out && \
+  ls out/OUT/assemblies.fa.gz && \
+  ls out/OUT/assembled_genes.fa.gz && \
+  ls out/OUT/assembled_seqs.fa.gz && \
+  ls out/OUT/log.clusters.gz && \
+  ls out/OUT/report.tsv && \
+  ls out/OUT/version_info.txt

ariba/2.14.7/README.md

@@ -0,0 +1,34 @@
+# ARIBA container
+
+Main tool: [ARIBA](https://github.com/sanger-pathogens/ariba)
+
+Additional tools:
+- [bowtie2](https://bowtie-bio.sourceforge.net/bowtie2/manual.shtml) 2.4.4
+- [SPAdes](https://github.com/ablab/spades) 3.13.1
+- [mummer](https://mummer.sourceforge.net/) 3.1
+- [cd-hit](https://sites.google.com/view/cd-hit) 4.8.1
+
+Full documentation: [https://github.com/sanger-pathogens/ariba/wiki](https://github.com/sanger-pathogens/ariba/wiki)
+
+Antimicrobial Resistance Identification By Assembly
+
+ARIBA is a tool that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling.
+
+The input is a FASTA file of reference sequences (can be a mix of genes and noncoding sequences) and paired sequencing reads. ARIBA reports which of the reference sequences were found, plus detailed information on the quality of the assemblies and any variants between the sequencing reads and the reference sequences.
+
+## Example Usage
+
+```bash
+# Get reference data, for instance from CARD
+ariba getref ncbi out.ncbi
+
+# Prepare reference data for ARIBA
+ariba prepareref -f out.ncbi.fa -m out.ncbi.tsv out.ncbi.prepareref
+
+# Run local assemblies and call variants
+ariba run out.ncbi.prepareref reads1.fastq reads2.fastq out.run
+
+#Summarise data from several runs
+ariba summary out.summary out.run1/report1.tsv out.run2/report2.tsv out.run3/report3.tsv
+```
+Please read the [ARIBA wiki page](https://github.com/sanger-pathogens/ariba/wiki) for full usage instructions.