From 2dafbe85eb6ccad0d0170bbc7156bb675f4d01eb Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 17 Dec 2024 14:01:10 -0700 Subject: [PATCH] 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 --- Program_Licenses.md | 1 + README.md | 1 + toulligqc/2.7.1/Dockerfile | 65 ++++++++++++++++++++++++++++++++++++++ toulligqc/2.7.1/README.md | 61 +++++++++++++++++++++++++++++++++++ 4 files changed, 128 insertions(+) create mode 100644 toulligqc/2.7.1/Dockerfile create mode 100644 toulligqc/2.7.1/README.md diff --git a/Program_Licenses.md b/Program_Licenses.md index 19af1594b..055259ea3 100644 --- a/Program_Licenses.md +++ b/Program_Licenses.md @@ -195,6 +195,7 @@ The licenses of the open-source software that is contained in these Docker image | TBProfiler | GNU GPLv3 | https://github.com/jodyphelan/TBProfiler/blob/master/LICENSE | | TipToft | GNU GPLv3 | https://github.com/andrewjpage/tiptoft/blob/master/LICENSE | | Tostadas | Apache-2.0 license | https://github.com/CDCgov/tostadas/blob/master/LICENSE | +| toulligqc | GNU GPLv3 | https://github.com/GenomiqueENS/toulligQC/blob/master/LICENSE.txt | | Treemmer | GNU GPLv3 | https://github.com/fmenardo/Treemmer/blob/master/COPYING | | Trimmomatic | GNU GPLv3 | https://github.com/usadellab/Trimmomatic/blob/main/distSrc/LICENSE | | Trycycler | GNU GPLv3 | https://github.com/rrwick/Trycycler/blob/master/LICENSE | diff --git a/README.md b/README.md index c00458f4f..4d879b3d4 100644 --- a/README.md +++ b/README.md @@ -307,6 +307,7 @@ To learn more about the docker pull rate limits and the open source software pro | [TBProfiler](https://hub.docker.com/r/staphb/tbprofiler/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/tbprofiler)](https://hub.docker.com/r/staphb/tbprofiler) | | https://github.com/jodyphelan/TBProfiler | | [TipToft](https://hub.docker.com/r/staphb/tiptoft/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/tiptoft)](https://hub.docker.com/r/staphb/tiptoft) | | https://github.com/andrewjpage/tiptoft | | [Tostadas](https://hub.docker.com/r/staphb/tostadas/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/tostadas)](https://hub.docker.com/r/staphb/tostadas) | | https://github.com/CDCgov/tostadas | +| [toulligQC](https://hub.docker.com/r/staphb/toulligqc/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/toulligqc)](https://hub.docker.com/r/staphb/toulligqc) | | https://github.com/GenomiqueENS/toulligQC | | [Treemmer](https://hub.docker.com/r/staphb/treemmer/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/treemmer)](https://hub.docker.com/r/staphb/treemmer) | | https://git.scicore.unibas.ch/TBRU/Treemmer (archived, moved to GitHub)
https://github.com/fmenardo/Treemmer | | [Trimmomatic](https://hub.docker.com/r/staphb/trimmomatic/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/trimmomatic)](https://hub.docker.com/r/staphb/trimmomatic) | | http://www.usadellab.org/cms/?page=trimmomatic
https://github.com/usadellab/Trimmomatic | | [Trycycler](https://hub.docker.com/r/staphb/trycycler/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/trycycler)](https://hub.docker.com/r/staphb/trycycler) | | https://github.com/rrwick/Trycycler | diff --git a/toulligqc/2.7.1/Dockerfile b/toulligqc/2.7.1/Dockerfile new file mode 100644 index 000000000..623177376 --- /dev/null +++ b/toulligqc/2.7.1/Dockerfile @@ -0,0 +1,65 @@ +FROM python:3.11.11-slim AS app + +ARG TOULIGQC_VER="2.7.1" + +# '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="${TOULIGQC_VER}" +LABEL description="QC analyses of Oxford Nanopore runs" +LABEL website="https://github.com/GenomiqueENS/toulligQC" +LABEL license="https://github.com/GenomiqueENS/toulligQC/blob/master/LICENSE.txt" +LABEL maintainer="Erin Young" +LABEL maintainer.email="eriny@utah.gov" + +# 'RUN' executes code during the build +# Install dependencies via apt-get or yum if using a centos or fedora base +RUN apt-get update && apt-get install -y --no-install-recommends \ + wget \ + ca-certificates\ + procps \ + bzip2 && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +RUN wget -q https://github.com/GenomiqueENS/toulligQC/archive/refs/tags/v${TOULIGQC_VER}.tar.gz && \ + pip install --no-cache-dir v${TOULIGQC_VER}.tar.gz && \ + rm -rf v${TOULIGQC_VER}.tar.gz + +# '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 + +# 'CMD' instructions set a default command when the container is run. This is typically 'tool --help.' +CMD [ "toulligqc", "--help" ] + +# 'WORKDIR' sets working directory +WORKDIR /data + +##### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ##### +##### 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. ##### +##### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ##### + +# A second FROM insruction creates a new stage +FROM app AS test + +ARG TOULIGQC_VER + +# set working directory so that all test inputs & outputs are kept in /test +WORKDIR /test + +# 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 + +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 diff --git a/toulligqc/2.7.1/README.md b/toulligqc/2.7.1/README.md new file mode 100644 index 000000000..c35f0e5c7 --- /dev/null +++ b/toulligqc/2.7.1/README.md @@ -0,0 +1,61 @@ +# toulligQC container + +Main tool: [toulligQC](https://github.com/GenomiqueENS/toulligQC) + +Code repository: https://github.com/GenomiqueENS/toulligQC + + +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 + +## Example Usage + +```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 + +# 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 + +# 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 + +# 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 + +# 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 +```