Update pbjasmine to 26.1.2

[cwoodside1278]

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

Updated pbjasmine (jasmine) to 26.1.2 version from 2.4.0

• Yes, this is true. Not sure why such a crazy jump.

• created new directory structure pbjasmine/26.1.2

• changed to Ubuntu:jammy to Ubuntu:noble

• Updated the container-specific read me to pbjasmine/26.1.2

• Updated the main read me to include the new version 26.1.2

Diff Output

diff -r pbjasmine/26.1.2/Dockerfile pbjasmine/2.4.0/Dockerfile
1c1
< FROM ubuntu:noble AS app
---
> FROM ubuntu:jammy AS app
3c3
< ARG JASMINE_VER="26.1.2"
---
> ARG JASMINE_VER="2.4.0"
5c5
< LABEL base.image="ubuntu:noble"
---
> LABEL base.image="ubuntu:jammy"

Test Build Output

Took a bit of time at the app stage.

[+] Building 435.8s (13/13) FINISHED                                                                                                                                  docker:default
 => [internal] load build definition from Dockerfile                                                                                                                            0.0s
 => => transferring dockerfile: 1.47kB                                                                                                                                          0.0s
 => [internal] load metadata for docker.io/library/ubuntu:noble                                                                                                                 0.0s
 => [internal] load metadata for docker.io/staphb/pbtk:3.1.1                                                                                                                    1.1s
 => [internal] load .dockerignore                                                                                                                                               0.0s
 => => transferring context: 2B                                                                                                                                                 0.0s
 => CACHED [app 1/4] FROM docker.io/library/ubuntu:noble@sha256:d1e2e92c075e5ca139d51a140fff46f84315c0fdce203eab2807c7e495eff4f9                                                0.0s
 => => resolve docker.io/library/ubuntu:noble@sha256:d1e2e92c075e5ca139d51a140fff46f84315c0fdce203eab2807c7e495eff4f9                                                           0.0s
 => [testdata 1/2] FROM docker.io/staphb/pbtk:3.1.1@sha256:a3d9dba71e3e25fe84d82295002eeac069668fb46cc47b94434f3d6bdfad0926                                                     2.0s
 => => resolve docker.io/staphb/pbtk:3.1.1@sha256:a3d9dba71e3e25fe84d82295002eeac069668fb46cc47b94434f3d6bdfad0926                                                              0.0s
 => => sha256:11891e954e57a76377ef1164a933fecca2dec982930857e41e804bd160104f06 93B / 93B                                                                                        0.3s
 => => sha256:3bc5cf069838dda2e45b3a96380f81ee8efd61fd0b540476c5adfe074036c9b6 12.75MB / 12.75MB                                                                                0.8s
 => => sha256:ac8495b661851ec5ff33f146637531d5653040e4f9eb791b449b71f27d748936 477.19kB / 477.19kB                                                                              0.5s
 => => sha256:bccd10f490ab0f3fba61b193d1b80af91b17ca9bdca9768a16ed05ce16552fcb 29.54MB / 29.54MB                                                                                0.8s
 => => extracting sha256:bccd10f490ab0f3fba61b193d1b80af91b17ca9bdca9768a16ed05ce16552fcb                                                                                       0.8s
 => => extracting sha256:ac8495b661851ec5ff33f146637531d5653040e4f9eb791b449b71f27d748936                                                                                       0.0s
 => => extracting sha256:3bc5cf069838dda2e45b3a96380f81ee8efd61fd0b540476c5adfe074036c9b6                                                                                       0.2s
 => => extracting sha256:11891e954e57a76377ef1164a933fecca2dec982930857e41e804bd160104f06                                                                                       0.0s
 => [app 2/4] RUN apt-get update && apt-get install --no-install-recommends -y     wget     xz-utils &&    apt-get autoclean && rm -rf /var/lib/apt/lists/*                    10.2s
 => [testdata 2/2] RUN wget -q --no-check-certificate https://downloads.pacbcloud.com/public/Sequel-II-CpG-training/CCS/methylated/m64168_200823_191315.hifi_reads.bam &&     427.9s
 => [app 3/4] RUN wget --no-check-certificate https://github.com/PacificBiosciences/jasmine/releases/download/v26.1.2/jasmine.tar.xz &&    tar -C /usr/local/ -xvf jasmine.tar  3.9s 
 => [app 4/4] WORKDIR /data                                                                                                                                                     0.3s 
 => [test 1/2] COPY --from=testdata /data/test.bam /data/test.bam                                                                                                               0.0s 
 => [test 2/2] RUN jasmine test.bam out.bam --log-level INFO                                                                                                                    1.9s 
 => exporting to image                                                                                                                                                          2.7s 
 => => exporting layers                                                                                                                                                         2.3s 
 => => exporting manifest sha256:c273a2ba1701ecb060875a48e7899543082eb6ffcaa88d36abd933e43c6426a1                                                                               0.0s 
 => => exporting config sha256:3431e3cf38a408c18861651b098411d397c4e4b4284b9caa587a7c8b8fc6756c                                                                                 0.0s 
 => => exporting attestation manifest sha256:4ac8f63b6407531011e8842449fa7544fcd7cc9f5bed9f48f7e7d880af27dcc9                                                                   0.0s 
 => => exporting manifest list sha256:1aa06bf569930988792aeee4f5afbd184cdb1fe271bcafaa807b25c90ce568bc                                                                          0.0s 
 => => naming to docker.io/library/pbjasmine:26.1.2                                                                                                                             0.0s
 => => unpacking to docker.io/library/pbjasmine:26.1.2                         

[erinyoung]

I have no changes to recommend

[erinyoung]

Tests worked

#14 [test 2/2] RUN jasmine test.bam out.bam --log-level INFO
#14 0.075 | 20260227 01:30:04.905 | INFO | Snapshot : (Legend) % CPU / Threads / ResMem GiB
#14 0.075 | 20260227 01:30:04.906 | INFO | Snapshot : 0.0% / 3T / 0.0G
#14 0.152 | 20260227 01:30:04.982 | WARN | Model (5mC) chemistry (R/P2-C3/5.0-25M) differs from data chemistry (S/P4-C2/5.0-8M)
#14 0.206 | 20260227 01:30:05.036 | WARN | Model (6mA) chemistry (R/P2-C3/5.0-25M) differs from data chemistry (S/P4-C2/5.0-8M)
#14 1.340 | 20260227 01:30:06.170 | INFO | 0 reads / 0 Bases
#14 1.641 | 20260227 01:30:06.471 | INFO | 10 reads / 84.8 KBases
#14 1.641 | 20260227 01:30:06.471 | INFO | Reads      : 10
#14 1.641 | 20260227 01:30:06.471 | INFO | Yield      : 84.8 KBases
#14 1.641 | 20260227 01:30:06.471 | INFO | Throughput : 3.9 MBases/min
#14 1.673 | 20260227 01:30:06.504 | INFO | Run Time : 1s 598ms 
#14 1.673 | 20260227 01:30:06.504 | INFO | CPU Time : 2s 816ms 
#14 1.674 | 20260227 01:30:06.504 | INFO | Peak RSS : 0.610 GB
#14 1.674 | 20260227 01:30:06.504 | INFO | Exit code : 0
#14 DONE 1.7s

[erinyoung]

Jasmine actually disappeared from github for a few week, too. It's one the repositories that I share with people trying to lecture me on "gold standard bioinformatics".

I'm going to merge this PR and get this deployed. Thank you for putting this together!

[erinyoung]

You can check the status of the deployment here : https://github.com/StaPH-B/docker-builds/actions/runs/22495339741