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add busco-prok with bacteria_odb #854
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| Original file line number | Diff line number | Diff line change |
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| ARG BUSCO_VER="5.6.1" | ||
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| FROM ubuntu:focal as app | ||
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| ARG BUSCO_VER | ||
| ARG BBMAP_VER="39.01" | ||
| ARG DEBIAN_FRONTEND=noninteractive | ||
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| LABEL base.image="ubuntu:focal" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="BUSCO" | ||
| LABEL software.version="${BUSCO_VER}" | ||
| LABEL description="Slim version of BUSCO for prokaryotes only" | ||
| LABEL website="https://busco.ezlab.org/" | ||
| LABEL license="https://gitlab.com/ezlab/busco/-/raw/master/LICENSE" | ||
| LABEL maintainer="Kutluhan Incekara" | ||
| LABEL maintainer.email="[email protected]" | ||
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| # install dependencies | ||
| RUN apt-get update && apt-get install --no-install-recommends -y \ | ||
| wget \ | ||
| python3-pip \ | ||
| python3-setuptools \ | ||
| python3-requests \ | ||
| python3-pandas \ | ||
| hmmer \ | ||
| prodigal \ | ||
| lbzip2 \ | ||
| openjdk-8-jre-headless \ | ||
| && rm -rf /var/lib/apt/lists/* && apt-get autoclean \ | ||
| && ln -s /usr/bin/python3 /usr/bin/python | ||
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| # BioPython (python3-biopython installs 1.73. It causes python error in this version) | ||
| RUN pip install --no-cache-dir biopython | ||
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| # bbtools | ||
| RUN wget https://sourceforge.net/projects/bbmap/files/BBMap_${BBMAP_VER}.tar.gz &&\ | ||
| tar -xvf BBMap_${BBMAP_VER}.tar.gz && rm BBMap_${BBMAP_VER}.tar.gz &&\ | ||
| mv /bbmap/* /usr/local/bin/ | ||
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| # sepp (greengenes version) | ||
| RUN wget https://raw.githubusercontent.com/smirarab/sepp-refs/54415e8905c5fa26cdd631c526b21f2bcdba95b5/gg/sepp-package.tar.bz &&\ | ||
| tar xvfj sepp-package.tar.bz && rm sepp-package.tar.bz &&\ | ||
| cd sepp-package/sepp &&\ | ||
| python setup.py config -c && chmod 755 run_* | ||
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| # busco | ||
| RUN wget https://gitlab.com/ezlab/busco/-/archive/${BUSCO_VER}/busco-${BUSCO_VER}.tar.gz &&\ | ||
| tar -xvf busco-${BUSCO_VER}.tar.gz && \ | ||
| rm busco-${BUSCO_VER}.tar.gz &&\ | ||
| cd busco-${BUSCO_VER} && \ | ||
| python3 setup.py install | ||
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| # download bacteria_odb10 | ||
| RUN mkdir data && cd data &&\ | ||
| busco --download bacteria_odb10 | ||
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| ENV PATH="${PATH}:/sepp-package/sepp" | ||
| ENV LC_ALL=C | ||
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| WORKDIR /data | ||
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| CMD busco -h | ||
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| ## Tests ## | ||
| FROM app as test | ||
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| # offline test | ||
| RUN wget -q 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 && \ | ||
| busco --offline -l bacteria_odb10 -m genome -i GCA_010941835.1_PDT000052640.3_genomic.fna -o offline --cpu 4 && \ | ||
| head offline/short_summary*.txt | ||
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| # auto-lineage-prok | ||
| RUN busco -m genome -i GCA_010941835.1_PDT000052640.3_genomic.fna -o auto --cpu 4 --auto-lineage-prok && \ | ||
| head auto/short_summary*.txt | ||
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| # Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO) container | ||
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| Main tool : [BUSCO](https://gitlab.com/ezlab/busco/) | ||
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| Additional tools: | ||
| - BBTools 39.01 | ||
| - HMMER 3.3 | ||
| - Prodigal 2.6.3 | ||
| - SEPP 4.5.1 | ||
| - Python 3.8.10 | ||
| - BioPython 1.83 | ||
| - Perl 5.30.0 | ||
| - OpenJDK 1.8.0_392 | ||
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| Full documentation: https://busco.ezlab.org/busco_userguide.html | ||
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| This is a BUSCO docker image which has basic functions for prokaryotes only. This image contains bacteria_odb10 lineage dataset for offline use. | ||
| ## Example Usage | ||
| ```bash | ||
| # offline usage with bacteria lineage | ||
| busco --offline -i assembly.fasta -l bacteria_odb10 -o output -m genome | ||
| # auto lineage selection | ||
| busco -i assembly.fasta -o output -m genome --auto-lineage-prok | ||
| ``` |
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I like that you include an offline test to make sure that it's working