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adding masurca version 4.1.2 #908
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,71 @@ | ||
| FROM ubuntu:jammy as app | ||
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| ARG MASURCA_VER="4.1.1" | ||
| ARG MINIMAP2_VER="2.24" | ||
| ARG BWA_VER="0.7.17" | ||
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| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="masurca" | ||
| LABEL software.version="${MASURCA_VER}" | ||
| LABEL description="Genome Assembly and Analysis" | ||
| LABEL website="https://github.com/alekseyzimin/masurca" | ||
| LABEL license="https://github.com/alekseyzimin/masurca/blob/master/LICENSE.txt" | ||
| LABEL maintainer="Erin Young" | ||
| LABEL maintainer.email="[email protected]" | ||
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| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| ca-certificates \ | ||
| #python \ | ||
| build-essential \ | ||
| curl \ | ||
| wget \ | ||
| gcc \ | ||
| zlib1g-dev \ | ||
| bzip2 \ | ||
| libboost-dev \ | ||
| libbz2-dev \ | ||
| liblzma-dev \ | ||
| numactl \ | ||
| procps \ | ||
| bwa && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| # install minimap2 | ||
| RUN curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VER}/minimap2-${MINIMAP2_VER}_x64-linux.tar.bz2 | tar -jxvf - --no-same-owner | ||
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| # install masurca suite | ||
| RUN mkdir /data && \ | ||
| wget https://github.com/alekseyzimin/masurca/releases/download/v$MASURCA_VER/MaSuRCA-$MASURCA_VER.tar.gz && \ | ||
| tar -xvf MaSuRCA-$MASURCA_VER.tar.gz && \ | ||
| tail /MaSuRCA-4.1.1/install.sh && \ | ||
| rm MaSuRCA-$MASURCA_VER.tar.gz | ||
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| WORKDIR /MaSuRCA-$MASURCA_VER | ||
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| # even in 4.1.1 there's the evil cp at the end of .install.sh | ||
| # This gives the error: | ||
| # 302.0 + cp -a ../Flye /MaSuRCA-4.1.1 | ||
| # 302.0 cp: '../Flye' and '/MaSuRCA-4.1.1/Flye' are the same file | ||
| RUN bash /MaSuRCA-$MASURCA_VER/install.sh 2>/dev/null ; exit 0 | ||
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| ENV PATH="${PATH}:/MaSuRCA-${MASURCA_VER}/Flye/bin:/MaSuRCA-${MASURCA_VER}/bin:/minimap2-${MINIMAP2_VER}_x64-linux:/bwa/bwa-${BWA_VER}" \ | ||
| LC_ALL=C | ||
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| # WORKDIR sets working directory | ||
| WORKDIR /data | ||
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| FROM app as test | ||
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| # testing POLCA | ||
| RUN wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123_1.fastq.gz && \ | ||
| wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123_2.fastq.gz && \ | ||
| wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.consensus.fa && \ | ||
| polca.sh -a SRR13957123.consensus.fa -r 'SRR13957123_1.fastq.gz SRR13957123_2.fastq.gz' && \ | ||
| test -f SRR13957123.consensus.fa.PolcaCorrected.fa | ||
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| # testing hybrid assembly | ||
| RUN wget -q https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/short_reads_1.fastq.gz && \ | ||
| wget -q https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/short_reads_2.fastq.gz && \ | ||
| wget -q https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/long_reads_low_depth.fastq.gz && \ | ||
| masurca -t 2 -i short_reads_1.fastq.gz,short_reads_2.fastq.gz -r long_reads_low_depth.fastq.gz |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,25 @@ | ||
| # masurca container | ||
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| Main tools: | ||
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| - [masurca](https://github.com/alekseyzimin/masurca) | ||
| - [polca](https://github.com/alekseyzimin/masurca#polca) | ||
| - [Chromosome scaffolder](https://github.com/alekseyzimin/masurca#chromosome-scaffolder) | ||
| - [SAMBA](https://github.com/alekseyzimin/masurca#samba-scaffolder) | ||
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| Other tools: | ||
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| - [bwa](https://github.com/lh3/bwa) (used by polca) 0.7.17-r1188 | ||
| - [minimap2](https://github.com/lh3/minimap2) (used by samba) 2.24-r1122 | ||
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| ## Example Usage | ||
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| ```bash | ||
| # masurca hybrid assembly | ||
| masurca -t 2 -i short_reads_1.fastq.gz,short_reads_2.fastq.gz -r long_reads.fastq.gz | ||
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| # polishes consensus genome with paired-end Illumina reads | ||
| polca.sh -a genome.fasta -r 'reads1.fastq reads2.fastq.gz' -t 16 -m 1G | ||
| ``` | ||
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| Better documentation can be found at [https://github.com/alekseyzimin/masurca](https://github.com/alekseyzimin/masurca) |
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thanks for adding all these relative links 👍