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Adding toulligqc version 2.7.1 (#1130)
* adding touligqc version 2.7.1 * adding toulligQC version 2.7.1 * adding toulligQC version 2.7.1 * added description * added no-cache-dir * added missing version * fixed paths
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| FROM python:3.11.11-slim AS app | ||
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| ARG TOULIGQC_VER="2.7.1" | ||
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| # 'LABEL' instructions tag the image with metadata that might be important to the user | ||
| LABEL base.image="python:3.11.11-slim" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="ToulligQC" | ||
| LABEL software.version="${TOULIGQC_VER}" | ||
| LABEL description="QC analyses of Oxford Nanopore runs" | ||
| LABEL website="https://github.com/GenomiqueENS/toulligQC" | ||
| LABEL license="https://github.com/GenomiqueENS/toulligQC/blob/master/LICENSE.txt" | ||
| LABEL maintainer="Erin Young" | ||
| LABEL maintainer.email="[email protected]" | ||
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| # 'RUN' executes code during the build | ||
| # Install dependencies via apt-get or yum if using a centos or fedora base | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| wget \ | ||
| ca-certificates\ | ||
| procps \ | ||
| bzip2 && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| RUN wget -q https://github.com/GenomiqueENS/toulligQC/archive/refs/tags/v${TOULIGQC_VER}.tar.gz && \ | ||
| pip install --no-cache-dir v${TOULIGQC_VER}.tar.gz && \ | ||
| rm -rf v${TOULIGQC_VER}.tar.gz | ||
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| # 'ENV' instructions set environment variables that persist from the build into the resulting image | ||
| # Use for e.g. $PATH and locale settings for compatibility with Singularity | ||
| ENV PATH="$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 [ "toulligqc", "--help" ] | ||
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| # 'WORKDIR' sets working directory | ||
| WORKDIR /data | ||
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| ##### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ##### | ||
| ##### Step 2. Set up the testing stage. ##### | ||
| ##### The docker image is built to the 'test' stage before merging, but ##### | ||
| ##### the test stage (or any stage after 'app') will be lost. ##### | ||
| ##### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ##### | ||
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| # A second FROM insruction creates a new stage | ||
| FROM app AS test | ||
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| ARG TOULIGQC_VER | ||
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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 toulligqc --help && \ | ||
| toulligqc --version | ||
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| RUN wget -q http://outils.genomique.biologie.ens.fr/leburon/downloads/toulligqc-example/toulligqc_demo_data.tar.bz2 && \ | ||
| tar -xvjf toulligqc_demo_data.tar.bz2 && \ | ||
| cd toulligqc_demo_data && \ | ||
| ./run-toulligqc.sh && \ | ||
| ls /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/report.html \ | ||
| /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/report.data \ | ||
| /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/*html |
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| # toulligQC container | ||
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| Main tool: [toulligQC](https://github.com/GenomiqueENS/toulligQC) | ||
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| Code repository: https://github.com/GenomiqueENS/toulligQC | ||
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| Basic information on how to use this tool: | ||
| - executable: toulligqc | ||
| - help: --help | ||
| - version: --version | ||
| - description: | | ||
| > ToulligQC is dedicated to the QC analyses of Oxford Nanopore runs. | ||
| Full documentation: https://github.com/GenomiqueENS/toulligQC | ||
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| ## Example Usage | ||
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| ```bash | ||
| # Sequencing summary alone | ||
| toulligqc --report-name summary_only \ | ||
| --sequencing-summary-source /path/to/basecaller/output/sequencing_summary.txt \ | ||
| --html-report-path /path/to/output/report.html | ||
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| # Sequencing summary + telemetry file | ||
| toulligqc --report-name summary_plus_telemetry \ | ||
| --telemetry-source /path/to/basecaller/output/sequencing_telemetry.js \ | ||
| --sequencing-summary-source /path/to/basecaller/output/sequencing_summary.txt \ | ||
| --html-report-path /path/to/output/report.html | ||
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| # Telemetry file + fast5 files | ||
| toulligqc --report-name telemetry_plus_fast5 \ | ||
| --telemetry-source /path/to/basecaller/output/sequencing_telemetry.js \ | ||
| --fast5-source /path/to/basecaller/output/fast5_files.fast5.gz \ | ||
| --html-report-path /path/to/output/report.html | ||
| # Fastq/ bam files only | ||
| toulligqc --report-name FAF0256 \ | ||
| --fastq /path/to/basecaller/output/fastq_files.fq.gz \ # (replace with --bam) | ||
| --html-report-path /path/to/output/report.html | ||
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| # Optional arguments for 1D² analysis | ||
| toulligqc --report-name FAF0256 \ | ||
| --telemetry-source /path/to/basecaller/output/sequencing_telemetry.js \ | ||
| --sequencing-summary-source /path/to/basecaller/output/sequencing_summary.txt \ | ||
| --sequencing-summary-1dsqr-source /path/to/basecaller/output/sequencing_1dsqr_summary.txt \ # (optional) | ||
| --html-report-path /path/to/output/report.html | ||
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| # Optional arguments to deal with barcoded samples | ||
| toulligqc --report-name FAF0256 \ | ||
| --barcoding \ | ||
| --telemetry-source /path/to/basecaller/output/sequencing_telemetry.js \ | ||
| --sequencing-summary-source /path/to/basecaller/output/sequencing_summary.txt \ | ||
| --sequencing-summary-source /path/to/basecaller/output/barcoding_summary_pass.txt \ # (optional) | ||
| --sequencing-summary-source /path/to/basecaller/output/barcoding_summary_fail.txt \ # (optional) | ||
| --sequencing-summary-1dsqr-source /path/to/basecaller/output/sequencing_1dsqr_summary.txt \ # (optional) | ||
| --sequencing-summary-1dsqr-source /path/to/basecaller/output/barcoding_summary_pass.txt \ # (optional) | ||
| --sequencing-summary-1dsqr-source /path/to/basecaller/output/barcoding_summary_fail.txt \ # (optional) | ||
| --html-report-path /path/to/output/report.html \ | ||
| --data-report-path /path/to/output/report.data \ # (optional) | ||
| --barcodes BC01,BC02,BC03 | ||
| ``` |