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Merge pull request #1113 from sage-wright/smw-polypolish-dev
add bwa to polypolish 0.6.0
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| ARG POLYPOLISH_VER="0.6.0" | ||
| ARG BWA_VER="0.7.18" | ||
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| FROM rust:1.75 AS builder | ||
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| ARG POLYPOLISH_VER | ||
| ARG BWA_VER | ||
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| RUN wget -q https://github.com/rrwick/Polypolish/archive/refs/tags/v${POLYPOLISH_VER}.tar.gz && \ | ||
| tar -vxf v${POLYPOLISH_VER}.tar.gz && \ | ||
| cd /Polypolish-${POLYPOLISH_VER} && \ | ||
| cargo build --release | ||
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| RUN wget https://github.com/lh3/bwa/archive/refs/tags/v${BWA_VER}.tar.gz &&\ | ||
| tar -xvf v${BWA_VER}.tar.gz &&\ | ||
| cd bwa-${BWA_VER} &&\ | ||
| make &&\ | ||
| mv bwa /usr/local/bin/ | ||
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| FROM ubuntu:jammy AS app | ||
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| ARG POLYPOLISH_VER | ||
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| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="polypolish" | ||
| LABEL software.version="${POLYPOLISH_VER}" | ||
| LABEL description="Polypolish is a tool for polishing genome assemblies with short reads." | ||
| LABEL website="https://github.com/rrwick/Polypolish" | ||
| LABEL license="https://github.com/rrwick/Polypolish/blob/main/LICENSE" | ||
| LABEL maintainer="Erin Young" | ||
| LABEL maintainer.email="[email protected]" | ||
| LABEL maintainer2="Sage Wright" | ||
| LABEL maintainer2.email="[email protected]" | ||
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| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| wget \ | ||
| ca-certificates \ | ||
| procps \ | ||
| unzip \ | ||
| python3 && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| COPY --from=builder /Polypolish-${POLYPOLISH_VER}/target/release/polypolish /usr/local/bin/polypolish | ||
| COPY --from=builder /usr/local/bin/bwa /usr/local/bin/ | ||
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| ENV LC_ALL=C | ||
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| CMD ["polypolish", "--help"] | ||
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| WORKDIR /data | ||
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| FROM app AS test | ||
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| RUN polypolish --help && polypolish --version | ||
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| # using "toy" data | ||
| RUN wget -q https://raw.githubusercontent.com/wiki/rrwick/Polypolish/files/toy_example/assembly.fasta && \ | ||
| wget -q https://raw.githubusercontent.com/wiki/rrwick/Polypolish/files/toy_example/alignments.sam && \ | ||
| polypolish polish assembly.fasta alignments.sam > polished.fasta | ||
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| # testing bwa | ||
| RUN wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR608/003/SRR6082043/SRR6082043_1.fastq.gz -O r1.fq.gz &&\ | ||
| wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR608/003/SRR6082043/SRR6082043_2.fastq.gz -O r2.fq.gz &&\ | ||
| wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/945/GCF_000006945.2_ASM694v2/GCF_000006945.2_ASM694v2_genomic.fna.gz &&\ | ||
| gunzip -c GCF_000006945.2_ASM694v2_genomic.fna.gz > ref.fa | ||
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| RUN bwa index ref.fa &&\ | ||
| bwa mem ref.fa r1.fq.gz r2.fq.gz > aln.sam &&\ | ||
| head aln.sam |
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| # polypolish container | ||
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| Main tool: [polypolish](https://github.com/rrwick/Polypolish/wiki/How-to-run-Polypolish) v0.6.0 | ||
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| Code repository: [polypolish](https://github.com/rrwick/Polypolish) | ||
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| Additional tools: | ||
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| - bwa: 0.7.18 | ||
| - python: 3.10 | ||
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| Basic information on how to use this tool: | ||
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| - executable: polypolish | ||
| - help: --help | ||
| - version: --version | ||
| - description: "Polypolish "polishes" consensus files created during assembly of long reads with Illumina short reads. Polypolish is a little different than other polishing tools in that paired-end reads need to be aligned separatly to generate two sam files." | ||
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| Additional information: This container also includes BWA v0.7.18 so that the user can align their short reads within the same container. | ||
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| Full documentation: [https://github.com/rrwick/Polypolish/wiki](https://github.com/rrwick/Polypolish/wiki) | ||
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| ## Example Usage | ||
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| Use the included bwa software to align reads to the draft sequence. Please note that bbamp, minimap2 or any other similar software can perform a similar step that may be better suited for your use-case. | ||
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| ```bash | ||
| bwa index draft.fasta | ||
| bwa mem -t 16 -a draft.fasta reads_1.fastq.gz > alignments_1.sam | ||
| bwa mem -t 16 -a draft.fasta reads_2.fastq.gz > alignments_2.sam | ||
| ``` | ||
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| Once the sam files are generated, they can be used with polypolish. | ||
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| ```bash | ||
| # paired end | ||
| polypolish filter --in1 alignments_1.sam --in2 alignments_2.sam --out1 filtered_1.sam --out2 filtered_2.sam | ||
| polypolish polish draft.fasta filtered_1.sam filtered_2.sam > polished.fasta | ||
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| # single end | ||
| polypolish polish draft.fasta input.sam > polished.fasta | ||
| ``` |