adding abricate version 1.2.0

[erinyoung]

There's a new version of abricate!

According to the release notes the database links are fixed and there are some new options.

Closes #1508

I copied the files from a prior version and updated the abricate version. I also updated the base image, added a CMD line, fixed the tests, and some other changes.

Also attached to this PR is a github action that will rebuild this image every month with whatever links abricate uses to download the databases.

The full diff:

$ diff build-files/abricate/{1.0.1-A*,1.2.0}/Dockerfile
1c1
< ARG ABRICATE_VER="1.0.1"
---
> ARG ABRICATE_VER="1.2.0"
3c3
< FROM ubuntu:focal as app
---
> FROM ubuntu:noble AS app
7c7
< ARG ANY2FASTA_VERSION="0.4.2"
---
> ARG ANY2FASTA_VERSION="0.8.1"
9c9
< LABEL base.image="ubuntu:focal"
---
> LABEL base.image="ubuntu:noble"
12c12
< LABEL software.version="1.0.1"
---
> LABEL software.version="${ABRICATE_VER}"
17a18,19
> LABEL maintainer2="Inês Mendes"
> LABEL maintainer2.email="[email protected]"
42,44c44,45
<   cd any2fasta-${ANY2FASTA_VERSION} && \
<   chmod +x any2fasta && \
<   cp any2fasta /usr/local/bin
---
>   cd /any2fasta-${ANY2FASTA_VERSION} && \
>   chmod +x any2fasta
50,51c51
<   mkdir /data && \
<   /abricate-${ABRICATE_VER}/bin/abricate --check
---
>   mkdir /data
55,56c55
< ENV PATH="/abricate-${ABRICATE_VER}/bin:\
< $PATH"\
---
> ENV PATH="/abricate-${ABRICATE_VER}/bin:/any2fasta-${ANY2FASTA_VERSION}:$PATH"\
59,64c58,59
< # add custom database; rename FASTA file as 'sequences'; index database with --setupdb
< ADD AcinetobacterPlasmidTyping.fasta /
< RUN mkdir -v /abricate-${ABRICATE_VER}/db/AcinetobacterPlasmidTyping && \
<   cp -v /AcinetobacterPlasmidTyping.fasta /abricate-${ABRICATE_VER}/db/AcinetobacterPlasmidTyping/sequences && \
<   abricate --setupdb && \
<   abricate --list
---
> # set up default databases
> RUN abricate --setupdb
70c65,69
< FROM app as test
---
> FROM app AS test
> 
> # Grab test Vcholerae genome, uncompress, and save to /data
> RUN wget -O - https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/018/083/565/GCA_018083565.2_PDT000793508.2/GCA_018083565.2_PDT000793508.2_genomic.fna.gz \
>   | gunzip -c > /data/GCA_018083565.2_PDT000793508.2_genomic.fna
78c77
< # tests shamelessly stolen and modified from: https://github.com/tseemann/abricate/blob/master/.travis.yml
---
> # tests shamelessly stolen and modified from: https://github.com/tseemann/abricate/blob/master/.github/workflows/ci.yml
80,104c79,106
< cd /abricate-${ABRICATE_VER}/ && \
< abricate --version && \
< abricate --help && \
< abricate --check && \
< abricate --list && \
< ! abricate --doesnotexist  && \
< ! abricate --threads 0 && \
< ! (abricate test/assembly.fa | grep '~~~') && \
< abricate test/assembly.fa > 1.tab && \
< abricate test/assembly.fa.gz > 2.tab && \
< abricate test/assembly.gbk > 3.tab && \
< abricate test/assembly.gbk.gz > 4.tab && \
< abricate --nopath test/assembly.gbk.gz | grep '^assembly.gbk.gz' && \
< abricate --summary {1,2,3,4}.tab > summary.tab && \
< abricate --summary 1.tab 2.tab 1.tab 2>&1 | grep 'duplicate' && \
< abricate --summary <(cat 1.tab 2.tab 3.tab) | wc -l | grep -w 4 && \
< abricate test/assembly.txt |& grep ERROR && \
< abricate not_exist.embl |& grep ERROR && \
< abricate --threads `nproc` test/assembly.fa.bz2 | grep -i FOSFOMYCIN && \
< abricate --threads `nproc` test/assembly.fa.bz2 | grep -i lactam && \
< for DB in `abricate --list | cut -f1 | tail -n +2`; do abricate --db ${DB} test/assembly.fa > /dev/null ; done && \
< abricate-get_db --help && \
< abricate-get_db --db ncbi --dbdir . && \
< ! grep 'FUSIDIC ACID' ncbi/sequences && \
< abricate --threads `nproc` --fofn test/fofn.txt
\ No newline at end of file
---
>   cd /abricate-${ABRICATE_VER}/ && \
>   abricate --setupdb
>   abricate --version
>   abricate --help
>   abricate --check
>   abricate --list
>   ! abricate --doesnotexist || echo "fail expected"
>   ! abricate --threads 0
>   ! (abricate test/assembly.fa | grep '~~~')
>   abricate test/assembly.fa > 1.tab
>   abricate test/assembly.fa.gz > 2.tab
>   abricate test/assembly.gbk > 3.tab
>   abricate test/assembly.gbk.gz > 4.tab
>   abricate --nopath test/assembly.gbk.gz | grep '^assembly.gbk.gz'
>   abricate --summary {1,2,3,4}.tab > summary.tab
>   abricate --summary 1.tab 2.tab 1.tab |& grep 'duplicate'
>   abricate --summary <(cat 1.tab 2.tab 3.tab) | wc -l | grep -w 4
>   abricate test/assembly.txt |& grep ERROR
>   abricate not_exist.embl |& grep ERROR
>   abricate --threads `nproc` test/assembly.fa.bz2 | grep -i FOSFOMYCIN
>   abricate --threads `nproc` test/assembly.fa.bz2 | grep -i lactam
>   for DB in `abricate --list | cut -f1 | tail -n +2`; do abricate --db $DB test/assembly.fa > /dev/null ; done
>   abricate-get_db --help
>   abricate-get_db --db ncbi --dbdir .
>   ! grep 'FUSIDIC ACID' ncbi/sequences
>   abricate --threads `nproc` --fofn test/fofn.txt
> 
> RUN abricate --list
\ No newline at end of file

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

[kapsakcj]

We can remove these 3 lines, they were for testing the custom V cholerae DB and are unnecessary here

[erinyoung]

I kept this one because this is a "real world" use-case. The rest of the tests use the toy data.

[erinyoung]

I have removed the github action, because it was pointed out to me that the databases are downloaded from the github repo, so rebuilding every month won't be useful.

[kapsakcj]

The most recent github actions workflow had all the docker image layers cached, so here's the one where it rebuilt the image from scratch, everything passed ✅ https://github.com/StaPH-B/docker-builds/actions/runs/20724012532/job/59495003575

some of the last few lines of output to show success:

#13 418.6 + grep 'FUSIDIC ACID' ncbi/sequences
#13 418.6 ++ nproc
#13 418.6 + abricate --threads 4 --fofn test/fofn.txt
#13 418.6 Using files from --fofn and ignoring any provided on the command line.
#13 418.7 Using nucl database ncbi:  8035 sequences -  2026-Jan-5
#13 418.7 Processing: test/assembly.fa
#13 418.7 #FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT	RESISTANCE
#13 421.1 Found 5 genes in test/assembly.fa
#13 421.1 test/assembly.fa	LGJG01000038	62416	62796	-	blaI_of_Z	1-381/381	===============	0/0	100.00	95.28	ncbi	NG_047499.1	penicillinase repressor BlaI	BETA-LACTAM
#13 421.1 test/assembly.fa	LGJG01000038	62786	64543	-	blaR1	1-1758/1758	===============	0/0	100.00	92.83	ncbi	NG_047539.1	beta-lactam sensor/signal transducer BlaR1	BETA-LACTAM
#13 421.1 test/assembly.fa	LGJG01000038	64650	65495	+	blaZ	1-846/846	===============	0/0	100.00	96.81	ncbi	NG_055999.1	penicillin-hydrolyzing class A beta-lactamase BlaZ	BETA-LACTAM
#13 421.1 test/assembly.fa	LGJG01000040	190796	191281	+	dfrS1	1-486/486	===============	0/0	100.00	99.38	ncbi	NG_077973.1	trimethoprim-resistant dihydrofolate reductase DfrS1	TRIMETHOPRIM
#13 421.1 test/assembly.fa	LGJG01000041	35416	35844	-	fosB-Sepi	1-429/429	===============	0/0	100.00	100.00	ncbi	NG_047889.1	FosB family fosfomycin resistance bacillithiol transferase	FOSFOMYCIN
#13 421.1 Tip: abricate can also find virulence factors; use --list to see all supported databases.
#13 421.1 Done.
#13 421.1 Processing: test/assembly.fa.bz2
#13 423.2 Found 5 genes in test/assembly.fa.bz2
#13 423.2 Tip: the abricate manual is at https://github.com/tseemann/abricate/blob/master/README.md
#13 423.2 Done.
#13 423.2 Processing: test/assembly.fa.gz
#13 423.2 test/assembly.fa.bz2	LGJG01000038	62416	62796	-	blaI_of_Z	1-381/381	===============	0/0	100.00	95.28	ncbi	NG_047499.1	penicillinase repressor BlaI	BETA-LACTAM
#13 423.2 test/assembly.fa.bz2	LGJG01000038	62786	64543	-	blaR1	1-1758/1758	===============	0/0	100.00	92.83	ncbi	NG_047539.1	beta-lactam sensor/signal transducer BlaR1	BETA-LACTAM
#13 423.2 test/assembly.fa.bz2	LGJG01000038	64650	65495	+	blaZ	1-846/846	===============	0/0	100.00	96.81	ncbi	NG_055999.1	penicillin-hydrolyzing class A beta-lactamase BlaZ	BETA-LACTAM
#13 423.2 test/assembly.fa.bz2	LGJG01000040	190796	191281	+	dfrS1	1-486/486	===============	0/0	100.00	99.38	ncbi	NG_077973.1	trimethoprim-resistant dihydrofolate reductase DfrS1	TRIMETHOPRIM
#13 423.2 test/assembly.fa.bz2	LGJG01000041	35416	35844	-	fosB-Sepi	1-429/429	===============	0/0	100.00	100.00	ncbi	NG_047889.1	FosB family fosfomycin resistance bacillithiol transferase	FOSFOMYCIN
#13 425.2 Found 5 genes in test/assembly.fa.gz
#13 425.2 Tip: found a bug in abricate? Post it at https://github.com/tseemann/abricate/issues.
#13 425.2 Done.
#13 425.2 Processing: test/assembly.gbk
#13 425.2 test/assembly.fa.gz	LGJG01000038	62416	62796	-	blaI_of_Z	1-381/381	===============	0/0	100.00	95.28	ncbi	NG_047499.1	penicillinase repressor BlaI	BETA-LACTAM
#13 425.2 test/assembly.fa.gz	LGJG01000038	62786	64543	-	blaR1	1-1758/1758	===============	0/0	100.00	92.83	ncbi	NG_047539.1	beta-lactam sensor/signal transducer BlaR1	BETA-LACTAM
#13 425.2 test/assembly.fa.gz	LGJG01000038	64650	65495	+	blaZ	1-846/846	===============	0/0	100.00	96.81	ncbi	NG_055999.1	penicillin-hydrolyzing class A beta-lactamase BlaZ	BETA-LACTAM
#13 425.2 test/assembly.fa.gz	LGJG01000040	190796	191281	+	dfrS1	1-486/486	===============	0/0	100.00	99.38	ncbi	NG_077973.1	trimethoprim-resistant dihydrofolate reductase DfrS1	TRIMETHOPRIM
#13 425.2 test/assembly.fa.gz	LGJG01000041	35416	35844	-	fosB-Sepi	1-429/429	===============	0/0	100.00	100.00	ncbi	NG_047889.1	FosB family fosfomycin resistance bacillithiol transferase	FOSFOMYCIN
#13 427.5 Found 5 genes in test/assembly.gbk
#13 427.5 Tip: the --fofn option allows you to feed in a big list of files to run on.
#13 427.5 Done.
#13 427.5 Processing: test/assembly.gbk.gz
#13 427.5 test/assembly.gbk	LGJG01000038	62416	62796	-	blaI_of_Z	1-381/381	===============	0/0	100.00	95.28	ncbi	NG_047499.1	penicillinase repressor BlaI	BETA-LACTAM
#13 427.5 test/assembly.gbk	LGJG01000038	62786	64543	-	blaR1	1-1758/1758	===============	0/0	100.00	92.83	ncbi	NG_047539.1	beta-lactam sensor/signal transducer BlaR1	BETA-LACTAM
#13 427.5 test/assembly.gbk	LGJG01000038	64650	65495	+	blaZ	1-846/846	===============	0/0	100.00	96.81	ncbi	NG_055999.1	penicillin-hydrolyzing class A beta-lactamase BlaZ	BETA-LACTAM
#13 427.5 test/assembly.gbk	LGJG01000040	190796	191281	+	dfrS1	1-486/486	===============	0/0	100.00	99.38	ncbi	NG_077973.1	trimethoprim-resistant dihydrofolate reductase DfrS1	TRIMETHOPRIM
#13 427.5 test/assembly.gbk	LGJG01000041	35416	35844	-	fosB-Sepi	1-429/429	===============	0/0	100.00	100.00	ncbi	NG_047889.1	FosB family fosfomycin resistance bacillithiol transferase	FOSFOMYCIN
#13 429.7 Found 5 genes in test/assembly.gbk.gz
#13 429.7 Tip: did you know? abricate was named after 'A'nti 'B'acterial 'R'esistiance
#13 429.7 Done.
#13 429.7 test/assembly.gbk.gz	LGJG01000038	62416	62796	-	blaI_of_Z	1-381/381	===============	0/0	100.00	95.28	ncbi	NG_047499.1	penicillinase repressor BlaI	BETA-LACTAM
#13 429.7 test/assembly.gbk.gz	LGJG01000038	62786	64543	-	blaR1	1-1758/1758	===============	0/0	100.00	92.83	ncbi	NG_047539.1	beta-lactam sensor/signal transducer BlaR1	BETA-LACTAM
#13 429.7 test/assembly.gbk.gz	LGJG01000038	64650	65495	+	blaZ	1-846/846	===============	0/0	100.00	96.81	ncbi	NG_055999.1	penicillin-hydrolyzing class A beta-lactamase BlaZ	BETA-LACTAM
#13 429.7 test/assembly.gbk.gz	LGJG01000040	190796	191281	+	dfrS1	1-486/486	===============	0/0	100.00	99.38	ncbi	NG_077973.1	trimethoprim-resistant dihydrofolate reductase DfrS1	TRIMETHOPRIM
#13 429.7 test/assembly.gbk.gz	LGJG01000041	35416	35844	-	fosB-Sepi	1-429/429	===============	0/0	100.00	100.00	ncbi	NG_047889.1	FosB family fosfomycin resistance bacillithiol transferase	FOSFOMYCIN
#13 DONE 429.7s

#14 [test 3/3] RUN abricate --list
#14 0.295 DATABASE	SEQUENCES	DBTYPE	DATE
#14 0.295 plasmidfinder	488	nucl	2026-Jan-5
#14 0.295 vfdb	4592	nucl	2026-Jan-5
#14 0.295 victors	4545	nucl	2026-Jan-5
#14 0.295 ecoh	597	nucl	2026-Jan-5
#14 0.295 bacmet2	746	prot	2026-Jan-5
#14 0.295 card	6052	nucl	2026-Jan-5
#14 0.295 ncbi	8035	nucl	2026-Jan-5
#14 0.295 argannot	2224	nucl	2026-Jan-5
#14 0.295 resfinder	3206	nucl	2026-Jan-5
#14 0.295 ecoli_vf	2701	nucl	2026-Jan-5
#14 0.295 megares	6635	nucl	2026-Jan-5
#14 DONE 0.3s

#15 exporting to docker image format
#15 exporting layers
#15 exporting layers 2.2s done
#15 exporting manifest sha256:f3e77b819ba315923f1cce2755920be6e41ff170970ad9972499b4f49d3435ac done
#15 exporting config sha256:f305dcc7b95fbe76eb7b0e86e765dd2bfd297105146334742eada554e9e7ebc4 done
#15 sending tarball
#15 sending tarball 4.9s done
#15 DONE 7.1s

[kapsakcj]

Thanks for the PR! Deploy workflow here: https://github.com/StaPH-B/docker-builds/actions/runs/20824656459