Tiptoft v1.0.2 Issue #526

[RaheelSyedAhmed]

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

This PR addresses issue #526 ; it includes an update to the dockerfile to have the standard stages present in Dockerfile (builder, app, test) and includes a new test case from the documentation. A program specific README.md has also been added with the packages used and the examples needed for users to update their database via the PlasmidFinder database and run tiptoft.

[erinyoung]

Tests still work

#16 [test 4/4] RUN mkdir /test/tiptoftDB &&     cd /test/tiptoftDB &&     DB_DATE=$(date +%Y-%m-%d) &&     tiptoft_database_downloader tiptoftDB-downloaded-on-${DB_DATE} &&     wget -q https://github.com/andrewjpage/tiptoft/raw/refs/heads/master/example_data/ERS654932_plasmids.fastq.gz &&     tiptoft -d /test/tiptoftDB/tiptoftDB-downloaded-on-${DB_DATE}.fa ERS654932_plasmids.fastq.gz
#16 0.174   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
#16 0.174                                  Dload  Upload   Total   Spent    Left  Speed
#16 0.174 
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 80757  100 80757    0     0   295k      0 --:--:-- --:--:-- --:--:--  296k
#16 0.450   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
#16 0.450                                  Dload  Upload   Total   Spent    Left  Speed
#16 0.450 
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 60460  100 60460    0     0   229k      0 --:--:-- --:--:-- --:--:--  228k
#16 0.717   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
#16 0.717                                  Dload  Upload   Total   Spent    Left  Speed
#16 0.717 
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  9307  100  9307    0     0  46535      0 --:--:-- --:--:-- --:--:-- 46535
#16 0.925   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
#16 0.925                                  Dload  Upload   Total   Spent    Left  Speed
#16 0.925 
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 66326  100 66326    0     0   286k      0 --:--:-- --:--:-- --:--:--  286k
#16 1.161   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
#16 1.161                                  Dload  Upload   Total   Spent    Left  Speed
#16 1.161 
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 15252  100 15252    0     0  64902      0 --:--:-- --:--:-- --:--:-- 64902
#16 1.405   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
#16 1.405                                  Dload  Upload   Total   Spent    Left  Speed
#16 1.405 
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 53608  100 53608    0     0   248k      0 --:--:-- --:--:-- --:--:--  246k
#16 1.626   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
#16 1.626                                  Dload  Upload   Total   Spent    Left  Speed
#16 1.626 
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 87238  100 87238    0     0   389k      0 --:--:-- --:--:-- --:--:--  389k
#16 1.854   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
#16 1.854                                  Dload  Upload   Total   Spent    Left  Speed
#16 1.854 
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  7829  100  7829    0     0  36078      0 --:--:-- --:--:-- --:--:-- 36078
#16 2.079   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
#16 2.079                                  Dload  Upload   Total   Spent    Left  Speed
#16 2.079 
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 36180  100 36180    0     0   166k      0 --:--:-- --:--:-- --:--:--  166k
#16 2.302 Downloading data with:
#16 2.302 curl -o enterobacteriales.fsa https://bitbucket.org/genomicepidemiology/plasmidfinder_db/raw/master/enterobacteriales.fsa
#16 2.302 Downloading data with:
#16 2.302 curl -o Inc18.fsa https://bitbucket.org/genomicepidemiology/plasmidfinder_db/raw/master/Inc18.fsa
#16 2.302 Downloading data with:
#16 2.302 curl -o NT_Rep.fsa https://bitbucket.org/genomicepidemiology/plasmidfinder_db/raw/master/NT_Rep.fsa
#16 2.302 Downloading data with:
#16 2.302 curl -o Rep1.fsa https://bitbucket.org/genomicepidemiology/plasmidfinder_db/raw/master/Rep1.fsa
#16 2.302 Downloading data with:
#16 2.302 curl -o Rep2.fsa https://bitbucket.org/genomicepidemiology/plasmidfinder_db/raw/master/Rep2.fsa
#16 2.302 Downloading data with:
#16 2.302 curl -o Rep3.fsa https://bitbucket.org/genomicepidemiology/plasmidfinder_db/raw/master/Rep3.fsa
#16 2.302 Downloading data with:
#16 2.302 curl -o RepA_N.fsa https://bitbucket.org/genomicepidemiology/plasmidfinder_db/raw/master/RepA_N.fsa
#16 2.302 Downloading data with:
#16 2.302 curl -o RepL.fsa https://bitbucket.org/genomicepidemiology/plasmidfinder_db/raw/master/RepL.fsa
#16 2.302 Downloading data with:
#16 2.302 curl -o Rep_trans.fsa https://bitbucket.org/genomicepidemiology/plasmidfinder_db/raw/master/Rep_trans.fsa
#16 2.302 Combining downloaded fasta files...
#16 2.302     Rep1.fsa
#16 2.302     Inc18.fsa
#16 2.302     NT_Rep.fsa
#16 2.302     Rep3.fsa
#16 2.302     enterobacteriales.fsa
#16 2.302     RepL.fsa
#16 2.302     RepA_N.fsa
#16 2.302     Rep_trans.fsa
#16 2.302     Rep2.fsa
#16 2.302 
#16 2.302 Finished combining files
#16 2.302 
#16 2.302 Finished. Final files are:
#16 2.302 	/test/tiptoftDB/tiptoftDB-downloaded-on-2026-06-03.fa
#16 2.302 	/test/tiptoftDB/tiptoftDB-downloaded-on-2026-06-03.tsv
#16 2.302 
#16 2.302 If you use this downloaded data, please cite:
#16 2.302 "PlasmidFinder and pMLST: in silico detection and typing
#16 2.302  of plasmids", Carattoli et al 2014, PMID: 24777092
#16 2.302 
#16 6.751 GENE	COMPLETENESS	%COVERAGE	ACCESSION	DATABASE	PRODUCT
#16 6.751 rep5b.3	Full	100	AE015935	plasmidfinder	rep5b.3_SEp608(pSE12228p06)_AE015935
#16 6.751 repUS76.1	Partial	97	AE015934	plasmidfinder	repUS76.1_rep(pSE12228p05)_AE015934
#16 6.751 rep20.11	Full	100	AP003367	plasmidfinder	rep20.11_repA(VRSAp)_AP003367
#16 6.751 rep7a.14	Full	100	NC007791	plasmidfinder	rep7a.14_CDS3(pUSA02)_NC007791
#16 6.751 rep7a.15	Full	100	AM990993	plasmidfinder	rep7a.15_repC(pS0385p1)_AM990993
#16 6.751 rep7a.16	Full	100	AB037671	plasmidfinder	rep7a.16_repC(Cassette)_AB037671
#16 6.751 rep7a.20	Full	100	AE015931	plasmidfinder	rep7a.20_SEp203(pSE12228p02)_AE015931
#16 6.751 ERS654932_plasmids.fastq.gz	16	180	2500	7.2
#16 DONE 6.8s

[erinyoung]

Can you adjust the tiptoft line in the main readme to include this tag?

[RaheelSyedAhmed]

Can you adjust the tiptoft line in the main readme to include this tag?

Yes, I've added a commit now to include 1.0.2-26 in the versions dropdown of the main README.md. Thank you for catching this!