Update staramr to 0.12.2

[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 staramr to 0.12.2 database from 0.12.1

• created new directory structure staramr/0.12.2
• Updated to python 3.14-slim from 3.12
• Updated the container specific readme at staramr/0.12.2
• Updated the main read me to include the new database

Local Test Build

[+] Building 79.2s (17/17) FINISHED                                                                                                                                   docker:default
 => [internal] load build definition from Dockerfile                                                                                                                            0.0s
 => => transferring dockerfile: 3.36kB                                                                                                                                          0.0s
 => [internal] load metadata for docker.io/library/python:3.14-slim                                                                                                             0.8s
 => [internal] load .dockerignore                                                                                                                                               0.0s
 => => transferring context: 2B                                                                                                                                                 0.0s
 => [app 1/7] FROM docker.io/library/python:3.14-slim@sha256:33ef7446e8c14b21cb247e23afbcdc90e98853b70812ca46b2265e769a7dfb8b                                                   3.0s
 => => resolve docker.io/library/python:3.14-slim@sha256:33ef7446e8c14b21cb247e23afbcdc90e98853b70812ca46b2265e769a7dfb8b                                                       0.0s
 => => sha256:69f581787942d1875d13a8581fb7e43f4cc7a02c48d63c562cdd6b2eb982ec3b 1.29MB / 1.29MB                                                                                  0.3s
 => => sha256:631be41052279d1b0eea2737fdcee1aaa2daf99c12f9bb6e44d6fd6b39d5780a 12.33MB / 12.33MB                                                                                0.6s
 => => sha256:33ef7446e8c14b21cb247e23afbcdc90e98853b70812ca46b2265e769a7dfb8b 10.37kB / 10.37kB                                                                                0.0s
 => => sha256:cb2a026931ad98548889f820f852e3399cdf45af067577baba5e06d222bd08d1 1.75kB / 1.75kB                                                                                  0.0s
 => => sha256:2e3f788256a7e2abe86eb972dd72d7bcdf4273f5d775817d2e3619170852559b 4.93kB / 4.93kB                                                                                  0.0s
 => => sha256:57fb71246055257a374deb7564ceca10f43c2352572b501efc08add5d24ebb61 29.78MB / 29.78MB                                                                                0.5s
 => => sha256:3b8271951027d7d23bc376966788b98653d0829af3929f77dbfdf82a98358e10 251B / 251B                                                                                      0.5s
 => => extracting sha256:57fb71246055257a374deb7564ceca10f43c2352572b501efc08add5d24ebb61                                                                                       1.3s
 => => extracting sha256:69f581787942d1875d13a8581fb7e43f4cc7a02c48d63c562cdd6b2eb982ec3b                                                                                       0.1s
 => => extracting sha256:631be41052279d1b0eea2737fdcee1aaa2daf99c12f9bb6e44d6fd6b39d5780a                                                                                       0.7s
 => => extracting sha256:3b8271951027d7d23bc376966788b98653d0829af3929f77dbfdf82a98358e10                                                                                       0.0s
 => [app 2/7] RUN apt-get update && apt-get install -y --no-install-recommends   git   wget   libmoo-perl   liblist-moreutils-perl   libjson-perl   gzip   file   ncbi-blast+  17.3s
 => [app 3/7] RUN wget -q https://github.com/tseemann/any2fasta/archive/refs/tags/v0.8.1.tar.gz &&     tar -xvf v0.8.1.tar.gz &&     rm v0.8.1.tar.gz &&     cd any2fasta-0.8.  3.0s 
 => [app 4/7] RUN wget -q https://github.com/tseemann/mlst/archive/v2.32.2.tar.gz &&   tar -xzf v2.32.2.tar.gz &&   rm v2.32.2.tar.gz                                           8.5s 
 => [app 5/7] RUN wget -q https://github.com/phac-nml/staramr/archive/refs/tags/0.12.2.tar.gz &&   pip install 0.12.2.tar.gz --no-cache-dir &&   rm -rf 0.12.2.tar.gz &&   mk  22.8s 
 => [app 6/7] RUN staramr db update -d && staramr db info                                                                                                                       6.1s 
 => [app 7/7] WORKDIR /data                                                                                                                                                     0.0s 
 => [test 1/6] RUN staramr --help && staramr --version                                                                                                                          1.6s 
 => [test 2/6] RUN wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/010/941/835/GCA_010941835.1_PDT000052640.3/GCA_010941835.1_PDT000052640.3_genomic.fna.gz  &&   gzip -d  0.7s 
 => [test 3/6] RUN staramr search -o /data/staramr-test-Salmonella   --pointfinder-organism salmonella   --plasmidfinder-database-type enterobacteriales   /data/GCA_010941835  7.1s 
 => [test 4/6] RUN apt-get update && apt-get install -y --no-install-recommends bsdmainutils                                                                                    4.7s 
 => [test 5/6] RUN column -t /data/staramr-test-Salmonella/mlst.tsv && echo &&   column -t /data/staramr-test-Salmonella/pointfinder.tsv && echo &&   column -t /data/staramr-  0.2s 
 => [test 6/6] RUN staramr db info                                                                                                                                              1.1s 
 => exporting to image                                                                                                                                                          2.4s 
 => => exporting layers                                                                                                                                                         2.3s 
 => => writing image sha256:0b30a6bf18d37d4b653cce48762fcbec3a7ee954cbdc2185e37ae99d5e1890b8                                                                                    0.0s 
 => => naming to docker.io/library/staramr:0.12.2                  

Diff Output

diff -r build-files/staramr/0.12.2/Dockerfile build-files/staramr/0.12.1/Dockerfile
2c2
< FROM python:3.14-slim AS app
---
> FROM python:3.12-slim AS app
4c4
< ARG STARAMR_VER="0.12.2"
---
> ARG STARAMR_VER="0.12.1"
8c8
< LABEL base.image="python:3.14-slim"
---
> LABEL base.image="python:3.12-slim"

[cwoodside1278]

@staphb-dockerbuilds-diff staramr 0.12.2 0.12.1

[github-actions]

Dockerfile Diff: staramr

Comparing: 0.12.2 -> 0.12.1

--- build-files/staramr/0.12.2/Dockerfile	2026-05-15 02:03:19.251174439 +0000
+++ build-files/staramr/0.12.1/Dockerfile	2026-05-15 02:03:19.251035186 +0000
@@ -1,11 +1,11 @@
 # base image
-FROM python:3.14-slim AS app
+FROM python:3.12-slim AS app
 
-ARG STARAMR_VER="0.12.2"
+ARG STARAMR_VER="0.12.1"
 ARG MLST_VER="2.32.2"
 ARG ANY2FASTA_VERSION="0.8.1"
 
-LABEL base.image="python:3.14-slim"
+LABEL base.image="python:3.12-slim"
 LABEL dockerfile.version="1"
 LABEL software="staramr"
 LABEL software.version="${STARAMR_VER}"