Toulligqc 2.8.4 by cwoodside1278 · Pull Request #1582 · StaPH-B/docker-builds

cwoodside1278 · 2026-03-08T19:24:40Z

Pull Request (PR) checklist:

Include a description of what is in this pull request in this message.
The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/build-files/samtools/1.15 )
Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number in build-files (i.e. docker-builds/build-files/spades/3.12.0/Dockerfile)
- (optional) All test files are located in same directory as the Dockerfile (i.e. build-files/shigatyper/2.0.1/test.sh)
Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. docker-builds/build-files/spades/3.12.0/README.md)
- If this README is longer than 30 lines, there is an explanation as to why more detail was needed
Dockerfile includes the recommended LABELS
Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

Description

This PR is for toulligqc update to 2.8.3

created new directory structure toulligqc/2.8.3
Updated the container-specific read me to toulligqc/2.8.3
Updated the main read me to include the new version

Diff output

diff -r 2.7.1/Dockerfile 2.8.3/Dockerfile
3c3
< ARG TOULIGQC_VER="2.7.1"
---
> ARG TOULIGQC_VER="2.8.3"

Test Build

[+] Building 393.4s (11/11) FINISHED                                                                                                                                  docker:default
 => [internal] load build definition from Dockerfile                                                                                                                            0.0s
 => => transferring dockerfile: 2.70kB                                                                                                                                          0.0s
 => [internal] load metadata for docker.io/library/python:3.11.11-slim                                                                                                          0.7s
 => [internal] load .dockerignore                                                                                                                                               0.0s
 => => transferring context: 2B                                                                                                                                                 0.0s
 => [app 1/4] FROM docker.io/library/python:3.11.11-slim@sha256:081075da77b2b55c23c088251026fb69a7b2bf92471e491ff5fd75c192fd38e5                                                2.3s
 => => resolve docker.io/library/python:3.11.11-slim@sha256:081075da77b2b55c23c088251026fb69a7b2bf92471e491ff5fd75c192fd38e5                                                    0.0s
 => => sha256:edba8d8f043953b561e79be40ade6c48f6c27b8b85dfac1165f80a1637fd7615 250B / 250B                                                                                      0.1s
 => => sha256:2bda8306c57d2c0711f7e7ec62755ed81678cf892fa73a364ec7d0c99b662dae 3.51MB / 3.51MB                                                                                  0.3s
 => => sha256:f6b3bbd679a5c905461f638a5dacbc1b24e449a401ce7760a5db83a69e189583 16.21MB / 16.21MB                                                                                0.4s
 => => sha256:8a628cdd7ccc83e90e5a95888fcb0ec24b991141176c515ad101f12d6433eb96 28.23MB / 28.23MB                                                                                0.6s
 => => extracting sha256:8a628cdd7ccc83e90e5a95888fcb0ec24b991141176c515ad101f12d6433eb96                                                                                       0.9s
 => => extracting sha256:2bda8306c57d2c0711f7e7ec62755ed81678cf892fa73a364ec7d0c99b662dae                                                                                       0.1s
 => => extracting sha256:f6b3bbd679a5c905461f638a5dacbc1b24e449a401ce7760a5db83a69e189583                                                                                       0.6s
 => => extracting sha256:edba8d8f043953b561e79be40ade6c48f6c27b8b85dfac1165f80a1637fd7615                                                                                       0.0s
 => [app 2/4] RUN apt-get update && apt-get install -y --no-install-recommends     wget     ca-certificates    procps     bzip2 &&     apt-get autoclean && rm -rf /var/lib/ap  8.6s
 => [app 3/4] RUN wget -q https://github.com/GenomiqueENS/toulligQC/archive/refs/tags/v2.8.3.tar.gz &&     pip install --no-cache-dir v2.8.3.tar.gz &&     rm -rf v2.8.3.tar.  61.6s 
 => [app 4/4] WORKDIR /data                                                                                                                                                     0.3s 
 => [test 1/3] WORKDIR /test                                                                                                                                                    0.0s 
 => [test 2/3] RUN toulligqc --help &&     toulligqc --version                                                                                                                  3.6s 
 => [test 3/3] RUN wget -q http://outils.genomique.biologie.ens.fr/leburon/downloads/toulligqc-example/toulligqc_demo_data.tar.bz2 &&     tar -xvjf toulligqc_demo_data.tar.  182.7s 
 => exporting to image                                                                                                                                                        133.3s 
 => => exporting layers                                                                                                                                                       104.2s 
 => => exporting manifest sha256:30f4f1b03bc236c8014b4be6a5a7e14837bc63cf33639970ca735566fdbe710a                                                                               0.0s 
 => => exporting config sha256:2508273d8a118d28a7cc0e0878ca0ed85cdfc891ebeda7ffa140cab1ee99d06b                                                                                 0.0s 
 => => exporting attestation manifest sha256:288d87ca10b8ca7620e80f76ef59080f76281984374297539df16476e91211e0                                                                   0.0s 
 => => exporting manifest list sha256:2c49bd7348b7c99667c1bed2fb2c684f5b6b9227fb3df48266e301d17d8fd079                                                                          0.0s 
 => => naming to docker.io/library/toulligqc:2.8.3                                                                                                                              0.0s
 => => unpacking to docker.io/library/toulligqc:2.8.3

…cker-builds into toulligqc-2.8.3

erinyoung · 2026-03-09T15:42:52Z

Does this warning matter?

#11 77.27 Warning: Barcode 'B0C7' is non-standard custom arrangement.
#11 93.45 Warning: The barcode B0C7 doesn't exist in input data

erinyoung · 2026-03-09T15:43:35Z

Otherwise, test seems to work

#11 [test 3/3] 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
#11 20.31 toulligqc_demo_data/
#11 20.31 toulligqc_demo_data/README
#11 20.31 toulligqc_demo_data/sequencing_telemetry.js
#11 20.35 toulligqc_demo_data/barcoding_summary_fail.txt
#11 23.65 toulligqc_demo_data/run-toulligqc.sh
#11 23.65 toulligqc_demo_data/barcoding_summary_pass.txt
#11 47.21 toulligqc_demo_data/run-toulligqc-with-docker.sh
#11 47.21 toulligqc_demo_data/sequencing_summary.txt
#11 77.27 Warning: Barcode 'B0C7' is non-standard custom arrangement.
#11 93.45 Warning: The barcode B0C7 doesn't exist in input data
#11 109.7 ToulligQC version 2.8.3
#11 109.7 * Initialize extractors
#11 109.7 * Start Toulligqc info extractor
#11 109.7 * End of Toulligqc info extractor (done in 0m0.00s)
#11 109.7 * Start Sequencing telemetry extractor
#11 109.7 * End of Sequencing telemetry extractor (done in 0m0.02s)
#11 109.7 * Start Basecaller sequencing summary extractor
#11 109.7   - Load sequencing summary file (67.13 MB used) in 0m14.68s
#11 109.7   - Extract info from sequencing summary file in 0m2.89s
#11 109.7   - Creation of image "Read count histogram" in 0m0.19s
#11 109.7   - Creation of image "Distribution of read lengths" in 0m1.34s
#11 109.7   - Creation of image "Yield plot through time" in 0m0.75s
#11 109.7   - Creation of image "PHRED score distribution" in 0m2.07s
#11 109.7   - Creation of image "PHRED score density distribution" in 0m0.36s
#11 109.7   - Creation of image "Channel occupancy of the flowcell" in 0m0.19s
#11 109.7   - Creation of image "Correlation between read length and PHRED score" in 0m0.95s
#11 109.7   - Creation of image "Read length over time" in 0m1.76s
#11 109.7   - Creation of image "PHRED score over time" in 0m1.97s
#11 109.7   - Creation of image "Translocation speed" in 0m1.99s
#11 109.7   - Creation of image "Pass barcoded reads distribution" in 0m0.05s
#11 109.7   - Creation of image "Fail barcoded reads distribution" in 0m0.08s
#11 109.7   - Creation of image "Read size distribution for barcodes" in 0m1.56s
#11 109.7   - Creation of image "PHRED score distribution for barcodes" in 0m1.52s
#11 109.7 * End of Basecaller sequencing summary extractor (done in 0m32.35s)
#11 109.7 * Write HTML report
#11 109.7 * Write statistics files
#11 109.7 * End of the QC extractor (done in 0m32.40s)
#11 109.9 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/Channel_occupancy_of_the_flowcell.html
#11 109.9 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/Correlation_between_read_length_and_PHRED_score.html
#11 109.9 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/Distribution_of_read_lengths.html
#11 109.9 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/Fail_barcoded_reads_distribution.html
#11 109.9 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/PHRED_score_density_distribution.html
#11 109.9 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/PHRED_score_distribution.html
#11 109.9 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/PHRED_score_distribution_for_barcodes.html
#11 109.9 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/PHRED_score_over_time.html
#11 109.9 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/Pass_barcoded_reads_distribution.html
#11 109.9 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/Read_count_histogram.html
#11 109.9 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/Read_length_over_time.html
#11 109.9 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/Read_size_distribution_for_barcodes.html
#11 109.9 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/Translocation_speed.html
#11 109.9 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/Yield_plot_through_time.html
#11 109.9 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/report.data
#11 109.9 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/report.html

erinyoung · 2026-03-09T15:44:39Z

This looks good to me, I just need to look up info about that warning to see if it's actually concerning.

cwoodside1278 · 2026-03-09T23:36:59Z

Agreed. I just don't know exactly what that means

erinyoung · 2026-03-10T15:29:21Z

It looks like there's a new version now that fixes these warnings. I vote we upgrade this PR to the latest version.

cwoodside1278 · 2026-03-11T21:12:57Z

Okay sounds good. I will work on it now.

cwoodside1278 · 2026-03-11T22:16:57Z

Alright, I updated everything to 2.8.4 and my test build worked fine. I am curious to see if this update fixes the issue:

[+] Building 553.9s (11/11) FINISHED                                                                                                                                  docker:default
 => [internal] load build definition from Dockerfile                                                                                                                            0.0s
 => => transferring dockerfile: 2.70kB                                                                                                                                          0.0s
 => [internal] load metadata for docker.io/library/python:3.11.11-slim                                                                                                          0.4s
 => [internal] load .dockerignore                                                                                                                                               0.0s
 => => transferring context: 2B                                                                                                                                                 0.0s
 => CACHED [app 1/4] FROM docker.io/library/python:3.11.11-slim@sha256:081075da77b2b55c23c088251026fb69a7b2bf92471e491ff5fd75c192fd38e5                                         0.0s
 => => resolve docker.io/library/python:3.11.11-slim@sha256:081075da77b2b55c23c088251026fb69a7b2bf92471e491ff5fd75c192fd38e5                                                    0.0s
 => [app 2/4] RUN apt-get update && apt-get install -y --no-install-recommends     wget     ca-certificates    procps     bzip2 &&     apt-get autoclean && rm -rf /var/lib/ap  9.6s
 => [app 3/4] RUN wget -q https://github.com/GenomiqueENS/toulligQC/archive/refs/tags/v2.8.4.tar.gz &&     pip install --no-cache-dir v2.8.4.tar.gz &&     rm -rf v2.8.4.tar.  64.4s 
 => [app 4/4] WORKDIR /data                                                                                                                                                     0.3s 
 => [test 1/3] WORKDIR /test                                                                                                                                                    0.0s 
 => [test 2/3] RUN toulligqc --help &&     toulligqc --version                                                                                                                  3.7s 
 => [test 3/3] RUN wget -q http://outils.genomique.biologie.ens.fr/leburon/downloads/toulligqc-example/toulligqc_demo_data.tar.bz2 &&     tar -xvjf toulligqc_demo_data.tar.  343.2s 
 => exporting to image                                                                                                                                                        132.1s 
 => => exporting layers                                                                                                                                                       103.4s 
 => => exporting manifest sha256:8a6cb6aed9f3cbcb7555bc0b7ed5cebadd829b964b1089116f67465ae070d142                                                                               0.0s 
 => => exporting config sha256:71c15e7c8b50e583b00b7ac8e3086dc98f13cc8eea4c74c0ad0dc8a05091be85                                                                                 0.0s 
 => => exporting attestation manifest sha256:ea7862e8f57775810e7b1555a979bf029bb80d583f44f6a520198d177af6fc22                                                                   0.0s 
 => => exporting manifest list sha256:e89f52be8e82ab12745c6a60bebe112004d84f47084df7cf63891b3ec4e445d5                                                                          0.0s 
 => => naming to docker.io/library/toulligqc:2.8.4                                                                                                                              0.0s
 => => unpacking to docker.io/library/toulligqc:2.8.4

erinyoung

Thank you for

changing the filepath
updating the hyperlink in the main README

erinyoung · 2026-03-12T16:52:04Z

The warning is still there, but I vote it's likely a small issue

#11 [test 3/3] 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
#11 18.78 toulligqc_demo_data/
#11 18.78 toulligqc_demo_data/README
#11 18.78 toulligqc_demo_data/sequencing_telemetry.js
#11 18.83 toulligqc_demo_data/barcoding_summary_fail.txt
#11 22.07 toulligqc_demo_data/run-toulligqc.sh
#11 22.07 toulligqc_demo_data/barcoding_summary_pass.txt
#11 45.52 toulligqc_demo_data/run-toulligqc-with-docker.sh
#11 45.52 toulligqc_demo_data/sequencing_summary.txt
#11 75.51 Warning: Barcode 'B0C7' is non-standard custom arrangement.
#11 92.08 Warning: The barcode B0C7 doesn't exist in input data
#11 108.4 ToulligQC version 2.8.4
#11 108.4 * Initialize extractors
#11 108.4 * Start Toulligqc info extractor
#11 108.4 * End of Toulligqc info extractor (done in 0m0.00s)
#11 108.4 * Start Sequencing telemetry extractor
#11 108.4 * End of Sequencing telemetry extractor (done in 0m0.02s)
#11 108.4 * Start Basecaller sequencing summary extractor
#11 108.4   - Load sequencing summary file (67.13 MB used) in 0m15.08s
#11 108.4   - Extract info from sequencing summary file in 0m2.89s
#11 108.4   - Creation of image "Read count histogram" in 0m0.20s
#11 108.4   - Creation of image "Distribution of read lengths" in 0m1.33s
#11 108.4   - Creation of image "Yield plot through time" in 0m0.75s
#11 108.4   - Creation of image "PHRED score distribution" in 0m2.07s
#11 108.4   - Creation of image "PHRED score density distribution" in 0m0.37s
#11 108.4   - Creation of image "Channel occupancy of the flowcell" in 0m0.20s
#11 108.4   - Creation of image "Correlation between read length and PHRED score" in 0m0.95s
#11 108.4   - Creation of image "Read length over time" in 0m1.76s
#11 108.4   - Creation of image "PHRED score over time" in 0m2.00s
#11 108.4   - Creation of image "Translocation speed" in 0m2.00s
#11 108.4   - Creation of image "Pass barcoded reads distribution" in 0m0.05s
#11 108.4   - Creation of image "Fail barcoded reads distribution" in 0m0.08s
#11 108.4   - Creation of image "Read size distribution for barcodes" in 0m1.57s
#11 108.4   - Creation of image "PHRED score distribution for barcodes" in 0m1.50s
#11 108.4 * End of Basecaller sequencing summary extractor (done in 0m32.80s)
#11 108.4 * Write HTML report
#11 108.4 * Write statistics files
#11 108.4 * End of the QC extractor (done in 0m32.86s)
#11 108.5 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/Channel_occupancy_of_the_flowcell.html
#11 108.5 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/Correlation_between_read_length_and_PHRED_score.html
#11 108.5 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/Distribution_of_read_lengths.html
#11 108.5 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/Fail_barcoded_reads_distribution.html
#11 108.5 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/PHRED_score_density_distribution.html
#11 108.5 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/PHRED_score_distribution.html
#11 108.5 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/PHRED_score_distribution_for_barcodes.html
#11 108.5 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/PHRED_score_over_time.html
#11 108.5 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/Pass_barcoded_reads_distribution.html
#11 108.5 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/Read_count_histogram.html
#11 108.5 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/Read_length_over_time.html
#11 108.5 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/Read_size_distribution_for_barcodes.html
#11 108.5 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/Translocation_speed.html
#11 108.5 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/Yield_plot_through_time.html
#11 108.5 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/report.data
#11 108.5 /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/report.html
#11 DONE 108.6s

erinyoung · 2026-03-12T16:53:05Z

Thank you for putting this together!

The status of the deployment can be found here : https://github.com/StaPH-B/docker-builds/actions/runs/23013590481

cwoodside1278 and others added 7 commits March 8, 2026 15:02

Create README.md for 2.8.3

ac66c0e

Merge branch 'StaPH-B:master' into toulligqc-2.8.3

bdb20d1

Create README.md

1ebd81d

Move 2.8.3 folder to correct location under toulligqc

f879495

Merge branch 'toulligqc-2.8.3' of https://github.com/cwoodside1278/do…

614932d

…cker-builds into toulligqc-2.8.3

Create Dockerfile to 2.8.3

3db9906

Update README.md to include 2.8.3

79d6076

cwoodside1278 and others added 3 commits March 11, 2026 17:58

Update Dockerfile from 2.8.3 to 2.8.4

49b986b

Update README.md from 2.8.3 to 2.8.4

9b8f472

Rename folder to 2.8.4

191cfba

erinyoung changed the title ~~Toulligqc 2.8.3~~ Toulligqc 2.8.4 Mar 12, 2026

erinyoung approved these changes Mar 12, 2026

View reviewed changes

erinyoung merged commit f1ce95b into StaPH-B:master Mar 12, 2026
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Toulligqc 2.8.4#1582

Toulligqc 2.8.4#1582
erinyoung merged 10 commits intoStaPH-B:masterfrom
cwoodside1278:toulligqc-2.8.3

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