add plasmidfinder 3.0.3

[Kincekara]

There is a new version. Hopefully resolves #1585
Removed .git files after db installation.

diff:

diff build-files/plasmidfinder/3.0.2 build-files/plasmidfinder/3.0.3
diff build-files/plasmidfinder/3.0.2/Dockerfile build-files/plasmidfinder/3.0.3/Dockerfile
5,12c5
< ARG PLASMIDFINDER_VER="3.0.2"
< # Sometimes does not get a proper version
< # If a commit does not have a verion, I think we should do what we do for the other *finder tools and use the latest commit
< # see here: https://bitbucket.org/genomicepidemiology/plasmidfinder_db/commits/4add282963c788762cdc3c6e91eb46c3d109f19b
< 
< # commit date: 2025-09-10
< ARG DB_COMMIT_HASH="49c24c1"
< # Feb 25, 2026 - using git clone in addition to the commit in order to download the database
---
> ARG PLASMIDFINDER_VER="3.0.3"
43,46c36,39
< RUN git clone https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git /database &&\
<     cd /database &&\
<     git checkout ${DB_COMMIT_HASH} &&\
<     python3 INSTALL.py kma_index
---
> RUN git clone -b plasmidfinder-${PLASMIDFINDER_VER} --depth 1 https://git@bitbucket.org/genomicepidemiology/plasmidfinder_db.git &&\
>     cd plasmidfinder_db &&\
>     python INSTALL.py &&\
>     rm -rf .git
56,57c49,50
<     CGE_PLASMIDFINDER_DB=/database \
<     PLASMID_DB=/database
---
>     CGE_PLASMIDFINDER_DB=/plasmidfinder_db \
>     PLASMID_DB=/plasmidfinder_db
diff build-files/plasmidfinder/3.0.2/README.md build-files/plasmidfinder/3.0.3/README.md
8c8
< - plasmidfinder_db : 2.2.0
---
> - plasmidfinder_db : plasmidfinder-3.0.3 (2.2.0)

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

[Kincekara]

@erinyoung, if you still get the error, we can try removing git as well.

[erinyoung]

plasmidfinder uses git at runtime, so we can't remove it.

I've tried adding the directory as a safe directory, but then I get a error: could not lock config file //.gitconfig: Permission denied

[Kincekara]

@erinyoung, could you check it again with the latest changes?

[erinyoung]

Works for me!

Also, tests work in GA actions.

#16 11.21 sbjct_header
#16 11.21 IncFIA_1__AP001918
#16 11.21 sbjct_header
#16 11.21 IncFIA_1__AP001918
#16 11.21 sbjct_header
#16 11.21 IncFII(pRSB107)_1__AJ851089
#16 11.21 sbjct_header
#16 11.21 IncFII(pRSB107)_1__AJ851089
#16 11.21 sbjct_header
#16 11.21 Col(MG828)_1__NC_008486
#16 11.21 sbjct_header
#16 11.21 Col(MG828)_1__NC_008486
#16 11.21 {
#16 11.21     "type": "software_result",
#16 11.21     "databases": {
#16 11.21         "PlasmidFinder-2.2.0": {
#16 11.21             "type": "database",
#16 11.21             "database_name": "PlasmidFinder",
#16 11.21             "database_version": "2.2.0",
#16 11.21             "key": "PlasmidFinder-2.2.0",
#16 11.21             "database_commit": "unknown"
#16 11.21         }
#16 11.21     },
#16 11.21     "seq_regions": {
#16 11.21         "IncFIA_1__AP001918": {
#16 11.21             "type": "seq_region",
#16 11.21             "phenotypes": [],
#16 11.21             "ref_database": "PlasmidFinder-2.2.0:enterobacteriales",
#16 11.21             "key": "IncFIA_1__AP001918",
#16 11.21             "gene": true,
#16 11.21             "name": "IncFIA",
#16 11.21             "identity": 100.0,
#16 11.21             "alignment_length": 388,
#16 11.21             "ref_seq_length": 388,
#16 11.21             "coverage": 100.0,
#16 11.21             "ref_acc": "NC008486",
#16 11.21             "ref_start_pos": 1,
#16 11.21             "ref_end_pos": 263,
#16 11.21             "query_id": "NA",
#16 11.21             "query_start_pos": "NA",
#16 11.21             "query_end_pos": "NA",
#16 11.21             "note": "",
#16 11.21             "query_string": "",
#16 11.21             "alignment_string": "",
#16 11.21             "ref_string": ""
#16 11.21         }
#16 11.21     },
#16 11.21     "seq_variations": {},
#16 11.21     "phenotypes": {},
#16 11.21     "software_executions": {
#16 11.21         "aad720484b2b3586ec9c0d5ad5eb9c739f129194": {
#16 11.21             "type": "software_exec",
#16 11.21             "command": "/usr/local/lib/python3.12/dist-packages/plasmidfinder/__main__.py -i ERR1937840.fastq -o test",
#16 11.21             "parameters": {
#16 11.21                 "infile": [
#16 11.21                     "ERR1937840.fastq"
#16 11.21                 ],
#16 11.21                 "outdir": "test",
#16 11.21                 "tmp_dir": null,
#16 11.21                 "method_path": null,
#16 11.21                 "db_path": "/plasmidfinder_db",
#16 11.21                 "databases": null,
#16 11.21                 "min_cov": 0.6,
#16 11.21                 "threshold": 0.9,
#16 11.21                 "extended_output": false,
#16 11.21                 "speciesinfo_json": null,
#16 11.21                 "quiet": false,
#16 11.21                 "out_json": null,
#16 11.21                 "legacy": false
#16 11.21             },
#16 11.21             "key": "aad720484b2b3586ec9c0d5ad5eb9c739f129194"
#16 11.21         }
#16 11.21     },
#16 11.21     "aln_hits": {},
#16 11.21     "software_name": "PlasmidFinder",
#16 11.21     "software_version": "3.0.3",
#16 11.21     "software_commit": "unknown",
#16 11.21     "run_date": "11.03.2026",
#16 11.21     "key": "PlasmidFinder-3.0.3"
#16 11.21 }

[erinyoung]

Thank you for working on this!

[Kincekara]

Future note:
If HOME is unset or the runtime user has no writable home, Git falls back to /.gitconfig. AWS runtimes mount / as read‑only, so Git throws: could not lock config file //.gitconfig: Permission denied.

[erinyoung]

I have no changes to recommend. Let's get this merged and deployed.

[erinyoung]

Thank you so much for getting this together!

The deploy link can be found here : https://github.com/StaPH-B/docker-builds/actions/runs/23009692166