Update Seqsender to 1.3.93 version

[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 seqsender to 1.3.93 from 1.3.9

• created new directory structure seqsender/1.3.93
• Updated the container-specific read me to seqsender/1.3.93
• Updated the main read me to include the new version

Diff Output

I sent a PR for 1.3.9, but since it hasn't been reviewed and merged with the main branch yet, I wasn't able to compare the two files. This is a comparison to the previous version 1.3.6.
diff -r build-files/seqsender/1.3.93/Dockerfile build-files/seqsender/1.3.6/Dockerfile

2c2
< FROM mambaorg/micromamba:2.5.0-ubuntu24.04 AS app
---
> FROM mambaorg/micromamba:2.4.0-ubuntu22.04 AS app
4c4
< ARG SEQSENDER_VERSION=1.3.93
---
> ARG SEQSENDER_VERSION=1.3.6
11c11
< LABEL base.image="mambaorg/micromamba:2.5.0-ubuntu24.04"
---
> LABEL base.image="mambaorg/micromamba:2.4.0-ubuntu22.04"
diff -r build-files/seqsender/1.3.93/README.md build-files/seqsender/1.3.6/README.md
1c1
< # SeqSender 1.3.93 container
---
> # SeqSender 1.3.3 container

Test Build Output

[+] Building 140.9s (13/13) FINISHED                                                                                                                                  docker:default
 => [internal] load build definition from Dockerfile                                                                                                                            0.0s
 => => transferring dockerfile: 2.54kB                                                                                                                                          0.0s
 => [internal] load metadata for docker.io/mambaorg/micromamba:2.5.0-ubuntu24.04                                                                                                0.3s
 => [internal] load .dockerignore                                                                                                                                               0.0s
 => => transferring context: 2B                                                                                                                                                 0.0s
 => CACHED [app 1/6] FROM docker.io/mambaorg/micromamba:2.5.0-ubuntu24.04@sha256:58b50f1c185d477f1b0d83ab10a38cce0adbfb647b3ee89a31568b40b38731a9                               0.0s
 => => resolve docker.io/mambaorg/micromamba:2.5.0-ubuntu24.04@sha256:58b50f1c185d477f1b0d83ab10a38cce0adbfb647b3ee89a31568b40b38731a9                                          0.0s
 => [app 2/6] RUN apt-get update && apt-get install -y --no-install-recommends     wget     ca-certificates     procps     libsqlite3-0 &&     apt-get autoclean && rm -rf /v  12.9s
 => [app 3/6] RUN wget -q https://github.com/CDCgov/seqsender/archive/refs/tags/v1.3.93.tar.gz &&   tar -xzf v1.3.93.tar.gz &&   rm -r v1.3.93.tar.gz &&   mkdir /data         39.4s
 => [app 4/6] RUN micromamba install --yes --name base -f "/seqsender-1.3.93/env.yaml" &&   micromamba clean --all --force-pkgs-dirs --yes                                     31.6s 
 => [app 5/6] WORKDIR /data                                                                                                                                                     0.1s 
 => [test 1/4] RUN seqsender.py --help &&   seqsender.py version |   grep "Version: 1.3.93" || exit 1                                                                           2.4s 
 => [test 2/4] RUN for org in FLU COV;   do seqsender.py test_data -bsng --organism "${org}" --submission_dir test_dir &&     test -d "test_dir/${org}_TEST_DATA/" || exit 1;   2.4s 
 => [test 3/4] RUN seqsender.py test_network_connection |   grep "No network connection issues detected" || exit 1                                                              4.1s 
 => [test 4/4] RUN micromamba list -n base                                                                                                                                      0.9s 
 => exporting to image                                                                                                                                                         46.5s 
 => => exporting layers                                                                                                                                                        36.0s 
 => => exporting manifest sha256:397a7c97ad297cd19dd89d40d0e558e93e3ae3eaa00ced3e7a00c40d0bfc8014                                                                               0.0s 
 => => exporting config sha256:600e809b64401829fa2be52f740f45e8d08b817bb7f7e2817671a65751057ff6                                                                                 0.0s 
 => => exporting attestation manifest sha256:eb23454ebc4eb7db28d2bbdcfa17725a2db232df4717cc65ca6497ebbaab1c32                                                                   0.0s 
 => => exporting manifest list sha256:7b50240f0dae0165d530c545beabbb65707203105edbfc8731ea832c4eae5913                                                                          0.0s 
 => => naming to docker.io/library/seqsender:1.3.93                                                                                                                             0.0s
 => => unpacking to docker.io/library/seqsender:1.3.93        

[erinyoung]

Tests worked

#11 [test 2/4] RUN for org in FLU COV;   do seqsender.py test_data -bsng --organism "${org}" --submission_dir test_dir &&     test -d "test_dir/${org}_TEST_DATA/" || exit 1;   done
#11 0.726 
#11 0.726 
#11 0.726 Generating submission test_data
#11 0.726 Files are stored at: /data/test_dir/FLU_TEST_DATA
#11 0.726 
#11 0.726 Total runtime (HRS:MIN:SECS): 0:00:00.014696
#11 1.432 
#11 1.432 
#11 1.432 Generating submission test_data
#11 1.432 Files are stored at: /data/test_dir/COV_TEST_DATA
#11 1.432 
#11 1.432 Total runtime (HRS:MIN:SECS): 0:00:00.012857
#11 DONE 1.5s

[erinyoung]

This PR has a file at build-files/docker-builds that I don't have permissions to move. Could this file be deleted?

[cwoodside1278]

@erinyoung Which file is it?

[erinyoung]

The file is build-files/docker-builds

[cwoodside1278]

Yes I see it you can delete it! Not sure where that came from. I can't delete it.

[erinyoung]

I can't delete it from the PR.

Can you try something like the following (on the command line)

# De-initialize the submodule
git submodule deinit -f build-files/docker-builds

# Remove it from the index
git rm -f build-files/docker-builds

# Remove leftover metadata
rm -rf .git/modules/build-files/docker-builds

# Remove entry from .gitmodules (if present)
# Edit .gitmodules and delete the section for that submodule

git add .gitmodules
git commit -m "Remove accidentally added submodule"

# Push back to this PR
git push

Please forgive any typos I may have introduced!

[cwoodside1278]

Okay I got it! It should be gone now @erinyoung

[erinyoung]

Thank you!

[erinyoung]

thank you for putting this together!

You can check the status of the deployment here : https://github.com/StaPH-B/docker-builds/actions/runs/22588147204