|
| 1 | +ARG METAMDBG_VER=1.4 |
| 2 | + |
| 3 | +FROM ubuntu:noble AS builder |
| 4 | +ARG METAMDBG_VER |
| 5 | + |
| 6 | +WORKDIR /opt |
| 7 | + |
| 8 | +RUN apt-get update && apt-get install -y --no-install-recommends \ |
| 9 | + wget \ |
| 10 | + ca-certificates \ |
| 11 | + build-essential \ |
| 12 | + cmake \ |
| 13 | + zlib1g-dev \ |
| 14 | + libomp-dev && \ |
| 15 | + apt-get autoclean && rm -rf /var/lib/apt/lists/* |
| 16 | + |
| 17 | +RUN wget -q https://github.com/GaetanBenoitDev/metaMDBG/archive/refs/tags/metaMDBG-${METAMDBG_VER}.tar.gz -O metaMDBG.tar.gz && \ |
| 18 | + mkdir metaMDBG && \ |
| 19 | + tar -xzf metaMDBG.tar.gz -C metaMDBG --strip-components=1 && \ |
| 20 | + rm metaMDBG.tar.gz && \ |
| 21 | + cd metaMDBG && \ |
| 22 | + mkdir build && \ |
| 23 | + cd build && \ |
| 24 | + cmake .. && \ |
| 25 | + make -j 3 && \ |
| 26 | + mv /opt/metaMDBG/build/bin/metaMDBG /usr/local/bin/metaMDBG |
| 27 | + |
| 28 | + |
| 29 | +FROM ubuntu:noble AS app |
| 30 | +ARG METAMDBG_VER |
| 31 | + |
| 32 | +LABEL base.image="ubuntu:noble" |
| 33 | +LABEL dockerfile.version="1" |
| 34 | +LABEL software="metaMDBG" |
| 35 | +LABEL software.version="${METAMDBG_VER}" |
| 36 | +LABEL description="A fast and memory-efficient assembler designed for long and accurate metagenomics reads (e.g. PacBio HiFi, Nanopore R10)." |
| 37 | +LABEL website="https://github.com/GaetanBenoitDev/metaMDBG" |
| 38 | +LABEL license="https://github.com/GaetanBenoitDev/metaMDBG/blob/main/LICENSE.md" |
| 39 | +LABEL maintainer="Raheel Ahmed" |
| 40 | +LABEL maintainer.email="raheelsyedahmed@gmail.com" |
| 41 | + |
| 42 | +COPY --from=builder /usr/local/bin/metaMDBG /usr/local/bin/metaMDBG |
| 43 | + |
| 44 | +RUN apt-get update && apt-get install -y --no-install-recommends \ |
| 45 | + libgomp1 && \ |
| 46 | + apt-get autoclean && rm -rf /var/lib/apt/lists/* |
| 47 | + |
| 48 | +ENV LC_ALL=C |
| 49 | + |
| 50 | +WORKDIR /data |
| 51 | + |
| 52 | +CMD [ "metaMDBG", "--help" ] |
| 53 | + |
| 54 | + |
| 55 | +FROM app AS test |
| 56 | + |
| 57 | +# set working directory so that all test inputs & outputs are kept in /test |
| 58 | +WORKDIR /test |
| 59 | + |
| 60 | +# metaMDBG --help and metaMDBG --version print out the same thing. |
| 61 | +RUN metaMDBG --help && \ |
| 62 | + metaMDBG asm --help && \ |
| 63 | + metaMDBG gfa --help |
| 64 | + |
| 65 | +RUN apt-get update && apt-get install -y --no-install-recommends \ |
| 66 | + wget \ |
| 67 | + ca-certificates && \ |
| 68 | + apt-get autoclean && rm -rf /var/lib/apt/lists/* |
| 69 | + |
| 70 | +RUN wget -q https://github.com/bactopia/bactopia-tests/raw/refs/heads/main/species/portiera/reads/nanopore/ERR3772599.fastq.gz && \ |
| 71 | + metaMDBG asm --out-dir ./ERR3772599/ --in-ont ERR3772599.fastq.gz --threads 8 && \ |
| 72 | + cd ERR3772599 && \ |
| 73 | + gunzip contigs.fasta.gz && \ |
| 74 | + head contigs.fasta |
| 75 | + |
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