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* adding ontime 0.2.3 * small fastq file
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| ARG ONTIME_VER="0.2.3" | ||
| ARG TARGET="x86_64-unknown-linux-musl" | ||
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| FROM rust:1.70 AS builder | ||
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| ARG ONTIME_VER | ||
| ARG TARGET | ||
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| RUN apt update \ | ||
| && apt install -y musl-tools | ||
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| RUN wget -q https://github.com/mbhall88/ontime/archive/refs/tags/${ONTIME_VER}.tar.gz && \ | ||
| tar zxf ${ONTIME_VER}.tar.gz && \ | ||
| rm ${ONTIME_VER}.tar.gz && \ | ||
| ls / && \ | ||
| cd /ontime-${ONTIME_VER} && \ | ||
| rustup target add "${TARGET}" && \ | ||
| cargo build --release --target "${TARGET}" && \ | ||
| strip target/${TARGET}/release/ontime | ||
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| FROM ubuntu:jammy as app | ||
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| ARG ONTIME_VER | ||
| ARG TARGET | ||
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| # 'LABEL' instructions tag the image with metadata that might be important to the user | ||
| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="ontime" | ||
| LABEL software.version="${ONTIME_VER}" | ||
| LABEL description="Filters nanopore reads by time" | ||
| LABEL website="https://github.com/mbhall88/ontime" | ||
| LABEL license="https://github.com/mbhall88/ontime/blob/main/LICENSE" | ||
| LABEL maintainer="Erin Young" | ||
| LABEL maintainer.email="[email protected]" | ||
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| COPY --from=builder /ontime-${ONTIME_VER}/target/${TARGET}/release/ontime /bin/ | ||
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| # for playing nice with workflow managers | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| ca-certificates \ | ||
| procps && \ | ||
| apt-get autoclean && \ | ||
| rm -rf /var/lib/apt/lists/* | ||
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| ENV PATH="$PATH" \ | ||
| LC_ALL=C | ||
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| # 'CMD' instructions set a default command when the container is run. This is typically 'tool --help.' | ||
| CMD ontime --help | ||
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| # 'WORKDIR' sets working directory | ||
| WORKDIR /data | ||
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| # A second FROM insruction creates a new stage | ||
| # The test stage must be downstream from 'app' | ||
| FROM app as test | ||
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| # set working directory so that all test inputs & outputs are kept in /test | ||
| WORKDIR /test | ||
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| # print help and version info; check dependencies (not all software has these options available) | ||
| # Mostly this ensures the tool of choice is in path and is executable | ||
| RUN ontime --help && \ | ||
| ontime --version | ||
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| COPY tests/test.fastq.gz . | ||
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| RUN ontime --to 1h test.fastq.gz -o ontime.test.txt && \ | ||
| head ontime.test.txt |
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| # ontime container | ||
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| Main tool: [ONTime](https://github.com/mbhall88/ontime/tree/main) | ||
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| Code repository: https://github.com/mbhall88/ontime | ||
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| Basic information on how to use this tool: | ||
| - executable: ontime | ||
| - help: --help | ||
| - version: --version | ||
| - description: Extracts nanopore reads based on when in the run reads were generated. | ||
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| Full documentation: https://github.com/mbhall88/ontime/tree/main | ||
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| WARNING : the nanopore fastq file MUST still have the time stamp on the reads in the fastq fime, so this tool is **NOT** expected to run on reads downloaded from public repositories. | ||
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| ## Example Usage | ||
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| ```bash | ||
| # reads from the first five hours | ||
| ontime --to 5h in.fq | ||
| # reads after the first 24 hours | ||
| ontime --from 24h in.fq | ||
| # Check what the earliest and latest start times in the fastq are | ||
| ontime --show in.fq | ||
| ``` | ||
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