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* adding medaka version 2.0.1 * minor changes to medaka dockerfile and readme; also updated run-singularity.yml to use a different runner and more importantly apptainer github action to see if it will appropriately test singularity/apptainer functionality --------- Co-authored-by: Curtis Kapsak <[email protected]>
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| ARG MEDAKA_VER="2.0.1" | ||
| ARG PYABPOA_VER="1.5.3" | ||
| ARG SAMTOOLS_VER="1.21" | ||
| ARG BCFTOOLS_VER=${SAMTOOLS_VER} | ||
| ARG HTSLIB_VER=${SAMTOOLS_VER} | ||
| ARG MINIMAP2_VER="2.28" | ||
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| FROM ubuntu:jammy AS builder | ||
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| ARG SAMTOOLS_VER | ||
| ARG BCFTOOLS_VER | ||
| ARG HTSLIB_VER | ||
| ARG MINIMAP2_VER | ||
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| # install dependencies required for compiling samtools | ||
| ARG DEBIAN_FRONTEND=noninteractive | ||
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| RUN apt-get update && apt-get install --no-install-recommends -y \ | ||
| libncurses5-dev \ | ||
| libbz2-dev \ | ||
| liblzma-dev \ | ||
| libcurl4-gnutls-dev \ | ||
| zlib1g-dev \ | ||
| libssl-dev \ | ||
| gcc \ | ||
| wget \ | ||
| make \ | ||
| perl \ | ||
| bzip2 \ | ||
| gnuplot \ | ||
| ca-certificates \ | ||
| curl \ | ||
| perl \ | ||
| bzip2 \ | ||
| autoconf \ | ||
| automake \ | ||
| make \ | ||
| gcc \ | ||
| libdeflate-dev \ | ||
| zlib1g-dev \ | ||
| libbz2-dev \ | ||
| liblzma-dev \ | ||
| libcurl4-gnutls-dev \ | ||
| libssl-dev \ | ||
| libperl-dev \ | ||
| libgsl0-dev \ | ||
| libdeflate-dev \ | ||
| procps && \ | ||
| rm -rf /var/lib/apt/lists/* && apt-get autoclean | ||
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| # download, compile, and install bcftools | ||
| RUN wget -q https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VER}/bcftools-${BCFTOOLS_VER}.tar.bz2 && \ | ||
| tar -xjf bcftools-${BCFTOOLS_VER}.tar.bz2 && \ | ||
| rm -v bcftools-${BCFTOOLS_VER}.tar.bz2 && \ | ||
| cd bcftools-${BCFTOOLS_VER} && \ | ||
| ./configure --enable-libgsl --enable-perl-filters &&\ | ||
| make && \ | ||
| make install | ||
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| # download, compile, and install samtools | ||
| RUN wget -q https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VER}/samtools-${SAMTOOLS_VER}.tar.bz2 && \ | ||
| tar -xjf samtools-${SAMTOOLS_VER}.tar.bz2 && \ | ||
| cd samtools-${SAMTOOLS_VER} && \ | ||
| ./configure && \ | ||
| make && \ | ||
| make install | ||
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| RUN wget -q https://github.com/samtools/htslib/releases/download/${HTSLIB_VER}/htslib-${HTSLIB_VER}.tar.bz2 && \ | ||
| tar -xjf htslib-${HTSLIB_VER}.tar.bz2 && \ | ||
| rm -v htslib-${HTSLIB_VER}.tar.bz2 && \ | ||
| cd htslib-${HTSLIB_VER} && \ | ||
| ./configure && \ | ||
| make && \ | ||
| make install | ||
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| RUN curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VER}/minimap2-${MINIMAP2_VER}_x64-linux.tar.bz2 | tar -jxvf - --no-same-owner && \ | ||
| mv -v minimap2-${MINIMAP2_VER}_x64-linux/minimap2 /usr/local/bin | ||
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| ### start of app stage ### | ||
| FROM ubuntu:jammy AS app | ||
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| ARG MEDAKA_VER | ||
| ARG PYABPOA_VER | ||
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| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version=1 | ||
| LABEL container.version="1" | ||
| LABEL software="Medaka" | ||
| LABEL software.version="${MEDAKA_VER}" | ||
| LABEL description="Consensus sequence correction provided by ONT Research" | ||
| LABEL website="https://github.com/nanoporetech/medaka" | ||
| LABEL license="https://github.com/nanoporetech/medaka/blob/master/LICENSE.md" | ||
| LABEL maintainer="Curtis Kapsak" | ||
| LABEL maintainer.email="[email protected]" | ||
| LABEL maintainer1="Erin Young" | ||
| LABEL maintainer1.email="[email protected]" | ||
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| ARG DEBIAN_FRONTEND=noninteractive | ||
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| # install dependencies required for running samtools | ||
| RUN apt-get update && apt-get install --no-install-recommends -y \ | ||
| perl \ | ||
| zlib1g \ | ||
| libncurses5 \ | ||
| bzip2 \ | ||
| libdeflate-dev \ | ||
| liblzma-dev \ | ||
| libcurl4-gnutls-dev \ | ||
| python3 \ | ||
| python3-pip \ | ||
| python-is-python3 \ | ||
| python3-dev \ | ||
| build-essential \ | ||
| libssl-dev \ | ||
| libffi-dev \ | ||
| libxml2-dev \ | ||
| libxslt1-dev \ | ||
| zlib1g-dev \ | ||
| libgsl-dev \ | ||
| && apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| # copy in samtools, htslib, and minimap2 executables from builder stage | ||
| COPY --from=builder /usr/local/bin/* /usr/local/bin/ | ||
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| # install medaka via pip | ||
| RUN pip install medaka-cpu==${MEDAKA_VER} --extra-index-url https://download.pytorch.org/whl/cpu --no-cache-dir && \ | ||
| pip install pyabpoa==${PYABPOA_VER} --no-cache-dir | ||
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| ENV LC_ALL=C | ||
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| # final working directory is /data | ||
| WORKDIR /data | ||
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| # default command is to pull up help options | ||
| CMD [ "medaka", "--help" ] | ||
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| ### start of test stage ### | ||
| FROM app AS test | ||
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| RUN apt-get update && apt-get install --no-install-recommends -y wget | ||
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| # making sure dependencies are in path | ||
| RUN samtools --help && minimap2 --help && tabix --help && bgzip --help | ||
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| RUN medaka --help && \ | ||
| medaka --version | ||
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| # set working directory so that all test inputs & outputs are kept in /test | ||
| WORKDIR /test | ||
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| # using on real data (CRPA isolate) | ||
| RUN wget -q https://www.ebi.ac.uk/ena/browser/api/fasta/GCA_021601745.3 -O GCA_021601745.3.fasta && \ | ||
| wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR234/068/SRR23473168/SRR23473168_1.fastq.gz && \ | ||
| medaka_consensus -i SRR23473168_1.fastq.gz -d GCA_021601745.3.fasta -o testing -t 4 | ||
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| # listing available models | ||
| RUN medaka tools list\_models |
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| # Medaka container | ||
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| Main tool : [medaka](https://github.com/nanoporetech/medaka) | ||
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| Additional tools: | ||
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| - bcftools version 1.21 | ||
| - samtools version 1.21 | ||
| - htslib version 1.21 | ||
| - minimap2 version 2.28 | ||
| - pyabpoa verson 1.5.3 | ||
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| Full documentation: [https://github.com/nanoporetech/medaka](https://github.com/nanoporetech/medaka) | ||
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| > medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. It provides state-of-the-art results outperforming sequence-graph based methods and signal-based methods, whilst also being faster. | ||
| ## Example Usage | ||
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| ```bash | ||
| # listing models | ||
| medaka tools list\_models | ||
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| # polishing | ||
| medaka_consensus -i sample.fastq.gz -d sample.fasta -o medaka/sample -t 4 | ||
| ``` | ||
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| ## Medaka models | ||
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| Medaka updates frequently. These are the medaka models in this image: | ||
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| ``` | ||
| Available: r103_fast_g507, r103_fast_snp_g507, r103_fast_variant_g507, r103_hac_g507, r103_hac_snp_g507, r103_hac_variant_g507, r103_sup_g507, r103_sup_snp_g507, r103_sup_variant_g507, r1041_e82_260bps_fast_g632, r1041_e82_260bps_fast_variant_g632, r1041_e82_260bps_hac_g632, r1041_e82_260bps_hac_v4.0.0, r1041_e82_260bps_hac_v4.1.0, r1041_e82_260bps_hac_variant_g632, r1041_e82_260bps_hac_variant_v4.1.0, r1041_e82_260bps_joint_apk_ulk_v5.0.0, r1041_e82_260bps_sup_g632, r1041_e82_260bps_sup_v4.0.0, r1041_e82_260bps_sup_v4.1.0, r1041_e82_260bps_sup_variant_g632, r1041_e82_260bps_sup_variant_v4.1.0, r1041_e82_400bps_bacterial_methylation, r1041_e82_400bps_fast_g615, r1041_e82_400bps_fast_g632, r1041_e82_400bps_fast_variant_g615, r1041_e82_400bps_fast_variant_g632, r1041_e82_400bps_hac_g615, r1041_e82_400bps_hac_g632, r1041_e82_400bps_hac_v4.0.0, r1041_e82_400bps_hac_v4.1.0, r1041_e82_400bps_hac_v4.2.0, r1041_e82_400bps_hac_v4.3.0, r1041_e82_400bps_hac_v5.0.0, r1041_e82_400bps_hac_variant_g615, r1041_e82_400bps_hac_variant_g632, r1041_e82_400bps_hac_variant_v4.1.0, r1041_e82_400bps_hac_variant_v4.2.0, r1041_e82_400bps_hac_variant_v4.3.0, r1041_e82_400bps_hac_variant_v5.0.0, r1041_e82_400bps_sup_g615, r1041_e82_400bps_sup_v4.0.0, r1041_e82_400bps_sup_v4.1.0, r1041_e82_400bps_sup_v4.2.0, r1041_e82_400bps_sup_v4.3.0, r1041_e82_400bps_sup_v5.0.0, r1041_e82_400bps_sup_variant_g615, r1041_e82_400bps_sup_variant_v4.1.0, r1041_e82_400bps_sup_variant_v4.2.0, r1041_e82_400bps_sup_variant_v4.3.0, r1041_e82_400bps_sup_variant_v5.0.0, r104_e81_fast_g5015, r104_e81_fast_variant_g5015, r104_e81_hac_g5015, r104_e81_hac_variant_g5015, r104_e81_sup_g5015, r104_e81_sup_g610, r104_e81_sup_variant_g610, r941_e81_fast_g514, r941_e81_fast_variant_g514, r941_e81_hac_g514, r941_e81_hac_variant_g514, r941_e81_sup_g514, r941_e81_sup_variant_g514, r941_min_fast_g507, r941_min_fast_snp_g507, r941_min_fast_variant_g507, r941_min_hac_g507, r941_min_hac_snp_g507, r941_min_hac_variant_g507, r941_min_sup_g507, r941_min_sup_snp_g507, r941_min_sup_variant_g507, r941_prom_fast_g507, r941_prom_fast_snp_g507, r941_prom_fast_variant_g507, r941_prom_hac_g507, r941_prom_hac_snp_g507, r941_prom_hac_variant_g507, r941_prom_sup_g507, r941_prom_sup_snp_g507, r941_prom_sup_variant_g507, r941_sup_plant_g610, r941_sup_plant_variant_g610 | ||
| Default consensus: r1041_e82_400bps_sup_v5.0.0 | ||
| Default variant: r1041_e82_400bps_sup_variant_v5.0.0 | ||
| ``` |