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adding trycycler 0.5.4 (StaPH-B#638)
* adding trycycler 0.5.4 * added env variable TERM so that warnings are silenced and test output looks pretty. Docker image builds and runs tests successfully --------- Co-authored-by: kapsakcj <[email protected]>
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| ARG TRYCYCLER_VER=0.5.4 | ||
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| FROM ubuntu:jammy as app | ||
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| ARG TRYCYCLER_VER | ||
| ARG MASH_VER=2.3 | ||
| ARG MINIASM_VER=0.3 | ||
| ARG MINIMAP2_VER=2.24 | ||
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| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="Trycycler" | ||
| LABEL software.version="${TRYCYCLER_VER}" | ||
| LABEL description="A tool for generating consensus long-read assemblies for bacterial genomes" | ||
| LABEL website="https://github.com/rrwick/Trycycler" | ||
| LABEL license="https://github.com/rrwick/Trycycler/blob/master/LICENSE" | ||
| LABEL maintainer="Erin Young" | ||
| LABEL maintainer.email="[email protected]" | ||
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| # install prerequisites, cleanup apt garbage | ||
| # muscle version: 3.8.31 | ||
| ARG DEBIAN_FRONTEND=noninteractive | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| python3 \ | ||
| python3-pip \ | ||
| gcc \ | ||
| wget \ | ||
| curl \ | ||
| bzip2 \ | ||
| build-essential \ | ||
| procps \ | ||
| ca-certificates \ | ||
| libz-dev \ | ||
| muscle \ | ||
| r-base \ | ||
| gfortran \ | ||
| libblas-dev \ | ||
| liblapack-dev && \ | ||
| apt-get clean && apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| # minimap2 | ||
| # apt deps: curl bzip2 | ||
| RUN curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VER}/minimap2-${MINIMAP2_VER}_x64-linux.tar.bz2 | tar -jxvf - | ||
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| # mash | ||
| RUN wget https://github.com/marbl/Mash/releases/download/v${MASH_VER}/mash-Linux64-v${MASH_VER}.tar && \ | ||
| tar -xvf mash-Linux64-v${MASH_VER}.tar && \ | ||
| rm -rf mash-Linux64-v${MASH_VER}.tar | ||
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| # miniasm | ||
| RUN wget https://github.com/lh3/miniasm/archive/v${MINIASM_VER}.tar.gz && \ | ||
| mkdir miniasm && \ | ||
| tar -xzvf v${MINIASM_VER}.tar.gz -C miniasm --strip-components 1 && \ | ||
| rm v${MINIASM_VER}.tar.gz && \ | ||
| cd miniasm && \ | ||
| make | ||
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| # install R packages | ||
| RUN R -e "install.packages(c('ape',\ | ||
| 'phangorn'),\ | ||
| repos = 'http://cran.us.r-project.org')" | ||
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| # Trycycler | ||
| # apt deps: muscle gcc | ||
| RUN wget https://github.com/rrwick/Trycycler/archive/v${TRYCYCLER_VER}.tar.gz && \ | ||
| tar -xzf v${TRYCYCLER_VER}.tar.gz && \ | ||
| rm v${TRYCYCLER_VER}.tar.gz && \ | ||
| pip3 install ./Trycycler-${TRYCYCLER_VER} Pillow && \ | ||
| mkdir /data | ||
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| # set /data as working directory | ||
| WORKDIR /data | ||
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| # set env PATH variable for installed programs | ||
| # LC_ALL for singularity compatibility | ||
| # TERM set so that output is pretty during tests and so warnings about TERM not being set are silenced | ||
| ENV PATH="/mash-Linux64-v${MASH_VER}:/minimap2-${MINIMAP2_VER}_x64-linux:/miniasm:${PATH}"\ | ||
| LC_ALL=C \ | ||
| TERM=xterm-256color | ||
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| FROM app as test | ||
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| ARG TRYCYCLER_VER | ||
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| WORKDIR /Trycycler-${TRYCYCLER_VER} | ||
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| RUN trycycler --help && trycycler --version | ||
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| RUN pytest |
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| # trycycler container | ||
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| Main tool: [trycycler](https://github.com/rrwick/Trycycler) | ||
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| Additional tools: | ||
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| - [miniasm](https://github.com/lh3/miniasm) 0.3-r179 | ||
| - [minimap2](https://github.com/lh3/minimap2) 2.24-r1122 | ||
| - [muscle](https://www.ebi.ac.uk/Tools/msa/muscle/) 3.8.1551 (recommended version) | ||
| - [mash](https://github.com/marbl/Mash) 2.3 | ||
| - R package ['ape'](https://cran.r-project.org/web/packages/ape/index.html) 5.7 | ||
| - R package ['phangorn'](https://cran.r-project.org/web/packages/phangorn/index.html) 2.11.1 | ||
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| Trycycler "tries" different assemblies to find the one most supported by long reads. | ||
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| ## Example Usage | ||
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| ```bash | ||
| trycycler subsample --reads reads.fastq --out_dir read_subsets | ||
| ``` | ||
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| ```bash | ||
| trycycler cluster --assemblies assemblies/*.fasta --reads reads.fastq --out_dir trycycler | ||
| ``` | ||
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| ```bash | ||
| trycycler reconcile --reads reads.fastq --cluster_dir trycycler/cluster_001 | ||
| ``` | ||
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| ```bash | ||
| trycycler consensus --cluster_dir trycycler/cluster_001 | ||
| ``` | ||
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| It is highly recommended to read Trycycler's [wiki](https://github.com/rrwick/Trycycler/wiki) for full usability and reasoning. |