From e8761ec50d16501f07971adef657f2884275ed3b Mon Sep 17 00:00:00 2001 From: Erin Young Date: Thu, 12 Dec 2024 00:04:10 +0000 Subject: [PATCH 1/7] adding touligqc version 2.7.1 --- toulligqc/2.7.1/Dockerfile | 64 ++++++++++++++++++++++++++++++++++++++ toulligqc/2.7.1/README.md | 62 ++++++++++++++++++++++++++++++++++++ 2 files changed, 126 insertions(+) create mode 100644 toulligqc/2.7.1/Dockerfile create mode 100644 toulligqc/2.7.1/README.md diff --git a/toulligqc/2.7.1/Dockerfile b/toulligqc/2.7.1/Dockerfile new file mode 100644 index 000000000..cededb17f --- /dev/null +++ b/toulligqc/2.7.1/Dockerfile @@ -0,0 +1,64 @@ +ARG TOULIGQC_VER="2.7.1" + +FROM python:3.11.11-slim as app + +ARG TOULIGQC_VER + +# '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="${TOULIGQC_VER}" +LABEL description="QC analyses of Oxford Nanopore runs" +LABEL website="https://github.com/GenomiqueENS/toulligQC" +LABEL license="https://github.com/GenomiqueENS/toulligQC/blob/master/LICENSE.txt" +LABEL maintainer="Erin Young" +LABEL maintainer.email="eriny@utah.gov" + +# 'RUN' executes code during the build +# Install dependencies via apt-get or yum if using a centos or fedora base +RUN apt-get update && apt-get install -y --no-install-recommends \ + wget \ + ca-certificates\ + procps && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +RUN wget -q https://github.com/GenomiqueENS/toulligQC/archive/refs/tags/v${TOULIGQC_VER}.tar.gz && \ + pip install 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 $ wget http://outils.genomique.biologie.ens.fr/leburon/downloads/toulligqc-example/toulligqc_demo_data.tar.bz2 && \ + tar -xzf toulligqc_demo_data.tar.bz2 && \ + cd toulligqc_demo_data && \ + ./run-toulligqc.sh && \ + ls RUN_ID/report.{html,data} RUN_ID/images/*{html,png} diff --git a/toulligqc/2.7.1/README.md b/toulligqc/2.7.1/README.md new file mode 100644 index 000000000..d205b147b --- /dev/null +++ b/toulligqc/2.7.1/README.md @@ -0,0 +1,62 @@ + + +# container + +Main tool: [](link to program) + +Code repository: + +Additional tools: +- list: version + +Basic information on how to use this tool: +- executable: +- help: <-h> +- version: <-v> +- description: + +Additional information: + + + +Full documentation: link to documentation or wiki + +## Example Usage + +```bash + +``` + + + From 0433a11d8ebd2e1648bd01164db68f4798375b82 Mon Sep 17 00:00:00 2001 From: Erin Young Date: Thu, 12 Dec 2024 21:48:42 +0000 Subject: [PATCH 2/7] adding toulligQC version 2.7.1 --- README.md | 1 + toulligqc/2.7.1/Dockerfile | 15 +++--- toulligqc/2.7.1/README.md | 98 +++++++++++++++++++------------------- 3 files changed, 56 insertions(+), 58 deletions(-) diff --git a/README.md b/README.md index 363353eed..88914d019 100644 --- a/README.md +++ b/README.md @@ -302,6 +302,7 @@ 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) |
  • [4.3.0](./tbprofiler/4.3.0/)
  • [4.4.0](./tbprofiler/4.4.0/)
  • [4.4.2](./tbprofiler/4.4.2/)
  • [5.0.1](tbprofiler/5.0.1/)
  • [6.2.0](tbprofiler/6.2.0/)
  • [6.2.1](tbprofiler/6.2.1/)
  • [6.3.0](tbprofiler/6.3.0/)
  • [6.4.0](tbprofiler/6.4.0/)
  • [6.4.1](tbprofiler/6.4.1/)
| 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) |
  • 1.0.0
  • 1.0.2
| 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) |
  • [0.2.0-beta](./tostadas/0.2.0-beta/)
  • [3.1.0](./tostadas/3.1.0/)
  • [4.0.0](./tostadas/4.0.0/)
| 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) |
  • [2.7.1](./toulligqc/2.7.1/)
| 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) |
  • 0.3
| 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) |
  • 0.38
  • 0.39
| 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) |
  • [0.3.1](./trycycler/0.3.1/)
  • [0.3.2](./trycycler/0.3.2/)
  • [0.3.3](./trycycler/0.3.3/)
  • [0.5.0](./trycycler/0.5.0/)
  • [0.5.3](./trycycler/0.5.3/)
  • [0.5.4](./trycycler/0.5.4/)
  • [0.5.5](./trycycler/0.5.5/)
| https://github.com/rrwick/Trycycler | diff --git a/toulligqc/2.7.1/Dockerfile b/toulligqc/2.7.1/Dockerfile index cededb17f..5739e69f2 100644 --- a/toulligqc/2.7.1/Dockerfile +++ b/toulligqc/2.7.1/Dockerfile @@ -1,6 +1,4 @@ -ARG TOULIGQC_VER="2.7.1" - -FROM python:3.11.11-slim as app +FROM python:3.11.11-slim AS app ARG TOULIGQC_VER @@ -20,7 +18,8 @@ LABEL maintainer.email="eriny@utah.gov" RUN apt-get update && apt-get install -y --no-install-recommends \ wget \ ca-certificates\ - procps && \ + 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 && \ @@ -45,7 +44,7 @@ WORKDIR /data ##### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ##### # A second FROM insruction creates a new stage -FROM app as test +FROM app AS test ARG TOULIGQC_VER @@ -57,8 +56,8 @@ WORKDIR /test RUN toulligqc --help && \ toulligqc --version -RUN wget -q $ wget http://outils.genomique.biologie.ens.fr/leburon/downloads/toulligqc-example/toulligqc_demo_data.tar.bz2 && \ - tar -xzf toulligqc_demo_data.tar.bz2 && \ +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 RUN_ID/report.{html,data} RUN_ID/images/*{html,png} + ls output/ToulligQC_Demo_Data/report.{html,data} output/ToulligQC_Demo_Data/images/*{html,png} diff --git a/toulligqc/2.7.1/README.md b/toulligqc/2.7.1/README.md index d205b147b..ca05b03a6 100644 --- a/toulligqc/2.7.1/README.md +++ b/toulligqc/2.7.1/README.md @@ -1,62 +1,60 @@ - - -# container - -Main tool: [](link to program) - -Code repository: - -Additional tools: -- list: version - -Basic information on how to use this tool: -- executable: -- help: <-h> -- version: <-v> -- description: - -Additional information: - - - -Full documentation: link to documentation or wiki - -## Example Usage - -```bash - -``` +# toulligQC container +Main tool: [toulligQC](https://github.com/GenomiqueENS/toulligQC) - +# 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 +``` From e6854cc3ff4a87be8fc02e7cc0924a1e3d242568 Mon Sep 17 00:00:00 2001 From: Erin Young Date: Thu, 12 Dec 2024 21:50:20 +0000 Subject: [PATCH 3/7] adding toulligQC version 2.7.1 --- Program_Licenses.md | 1 + 1 file changed, 1 insertion(+) diff --git a/Program_Licenses.md b/Program_Licenses.md index d57e19474..7f22dea6d 100644 --- a/Program_Licenses.md +++ b/Program_Licenses.md @@ -190,6 +190,7 @@ 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 | From 05b76e0e81cb366b820c35bcec5d82c7888bf050 Mon Sep 17 00:00:00 2001 From: Erin Young Date: Thu, 12 Dec 2024 21:52:16 +0000 Subject: [PATCH 4/7] added description --- toulligqc/2.7.1/README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/toulligqc/2.7.1/README.md b/toulligqc/2.7.1/README.md index ca05b03a6..c35f0e5c7 100644 --- a/toulligqc/2.7.1/README.md +++ b/toulligqc/2.7.1/README.md @@ -9,7 +9,8 @@ Basic information on how to use this tool: - executable: toulligqc - help: --help - version: --version -- description: +- description: | +> ToulligQC is dedicated to the QC analyses of Oxford Nanopore runs. Full documentation: https://github.com/GenomiqueENS/toulligQC From 1abcd7b9a41ae6c4c49ee33f3a00e280f9be09ac Mon Sep 17 00:00:00 2001 From: Erin Young Date: Thu, 12 Dec 2024 21:53:01 +0000 Subject: [PATCH 5/7] added no-cache-dir --- toulligqc/2.7.1/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/toulligqc/2.7.1/Dockerfile b/toulligqc/2.7.1/Dockerfile index 5739e69f2..3ab3e1beb 100644 --- a/toulligqc/2.7.1/Dockerfile +++ b/toulligqc/2.7.1/Dockerfile @@ -23,7 +23,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ apt-get autoclean && rm -rf /var/lib/apt/lists/* RUN wget -q https://github.com/GenomiqueENS/toulligQC/archive/refs/tags/v${TOULIGQC_VER}.tar.gz && \ - pip install v${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 From 3a7a62956fba3844097f3313fc826c76c9fd8bed Mon Sep 17 00:00:00 2001 From: Erin Young Date: Thu, 12 Dec 2024 22:02:40 +0000 Subject: [PATCH 6/7] added missing version --- toulligqc/2.7.1/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/toulligqc/2.7.1/Dockerfile b/toulligqc/2.7.1/Dockerfile index 3ab3e1beb..ddf74d8f9 100644 --- a/toulligqc/2.7.1/Dockerfile +++ b/toulligqc/2.7.1/Dockerfile @@ -1,6 +1,6 @@ FROM python:3.11.11-slim AS app -ARG TOULIGQC_VER +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" From 72e91ccbba9ea6f5a3fd7f6282db86d150e07794 Mon Sep 17 00:00:00 2001 From: Erin Young Date: Thu, 12 Dec 2024 22:49:06 +0000 Subject: [PATCH 7/7] fixed paths --- toulligqc/2.7.1/Dockerfile | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/toulligqc/2.7.1/Dockerfile b/toulligqc/2.7.1/Dockerfile index ddf74d8f9..623177376 100644 --- a/toulligqc/2.7.1/Dockerfile +++ b/toulligqc/2.7.1/Dockerfile @@ -60,4 +60,6 @@ RUN wget -q http://outils.genomique.biologie.ens.fr/leburon/downloads/toulligqc- tar -xvjf toulligqc_demo_data.tar.bz2 && \ cd toulligqc_demo_data && \ ./run-toulligqc.sh && \ - ls output/ToulligQC_Demo_Data/report.{html,data} output/ToulligQC_Demo_Data/images/*{html,png} + 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