From beb5349b5c0d857b9f868274f502c14e9a1ffdcd Mon Sep 17 00:00:00 2001 From: Curtis Kapsak Date: Thu, 7 Nov 2024 16:42:39 +0000 Subject: [PATCH 1/5] added dockerfile for amrfinderplus 4.0.3 and db 2024-10-22.1. also added readme --- .../4.0.3-2024-10-22.1/Dockerfile | 100 ++++++++++++++++++ .../4.0.3-2024-10-22.1/README.md | 69 ++++++++++++ 2 files changed, 169 insertions(+) create mode 100755 ncbi-amrfinderplus/4.0.3-2024-10-22.1/Dockerfile create mode 100755 ncbi-amrfinderplus/4.0.3-2024-10-22.1/README.md diff --git a/ncbi-amrfinderplus/4.0.3-2024-10-22.1/Dockerfile b/ncbi-amrfinderplus/4.0.3-2024-10-22.1/Dockerfile new file mode 100755 index 000000000..49e9facfb --- /dev/null +++ b/ncbi-amrfinderplus/4.0.3-2024-10-22.1/Dockerfile @@ -0,0 +1,100 @@ +FROM ubuntu:jammy AS app + +ARG AMRFINDER_VER="4.0.3" +ARG AMRFINDER_DB_VER="2024-10-22.1" +ARG BLAST_VER="2.16.0" + +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="NCBI AMRFinderPlus" +LABEL software.version="${AMRFINDER_VER}" +LABEL description="NCBI resistance gene detection tool" +LABEL website="https://github.com/ncbi/amr" +LABEL license="https://github.com/ncbi/amr/blob/master/LICENSE" +LABEL maintainer="Kelsey Florek" +LABEL maintainer.email="kelsey.florek@slh.wisc.edu" +LABEL maintainer2="Curtis Kapsak" +LABEL maintainer2.email="kapsakcj@gmail.com" +LABEL maintainer3="Anders Goncalves da Silva" +LABEL maintainer3.email="andersgs@gmail.com" +LABEL maintainer4="Erin Young" +LABEL maintainer4.email="eriny@utah.gov" +LABEL maintainer5="Holly McQueary" +LABEL maintainer5.email="holly.c.mcqueary@mass.gov" + +# ncbi-blast+ installed via apt is v2.12.0 - DISABLING so that we can manually install a more recent version +# see here for reason why I'm manualy installing 2.14.0 instead of using apt-get: https://github.com/ncbi/amr/releases/tag/amrfinder_v3.11.8 + +# hmmer installed via apt is v3.3.2 +# removed because likely unnecessary since we are not compiling from source: make g++ +# libgomp1 required for makeblastdb +RUN apt-get update && apt-get install -y --no-install-recommends \ + ca-certificates \ + wget \ + curl \ + libgomp1 \ + hmmer \ + procps \ + gzip && \ + apt-get autoclean && \ + rm -rf /var/lib/apt/lists/* + +# download and install amrfinderplus pre-compiled binaries; make /data +RUN mkdir amrfinder && cd /amrfinder && \ + echo "downloading amrfinderplus v${AMRFINDER_VER} pre-compiled binaries from GitHub..." && \ + wget -q https://github.com/ncbi/amr/releases/download/amrfinder_v${AMRFINDER_VER}/amrfinder_binaries_v${AMRFINDER_VER}.tar.gz && \ + tar zxf amrfinder_binaries_v${AMRFINDER_VER}.tar.gz && \ + rm -v amrfinder_binaries_v${AMRFINDER_VER}.tar.gz && \ + mkdir -v /data + +# install ncbi-blast linux binaries +RUN echo "downloading ncbi-blast-${BLAST_VER}+ linux binaries from NCBI FTP..." && \ + wget -q https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLAST_VER}/ncbi-blast-${BLAST_VER}+-x64-linux.tar.gz && \ + tar -xzf ncbi-blast-${BLAST_VER}+-x64-linux.tar.gz && \ + rm -v ncbi-blast-${BLAST_VER}+-x64-linux.tar.gz + +# set PATH and locale settings for singularity compatibiliity, set amrfinder and manually-installed blast as higher priority in PATH +ENV PATH="/amrfinder:/ncbi-blast-${BLAST_VER}+/bin:$PATH" \ + LC_ALL=C + +# download databases and index them +# done in this manner to pin the database version instead of pulling the latest version with `amrfinder -u` +# softlink is required for `amrfinder -l` and typical `amrfinder` use cases to work properly +RUN mkdir -p /amrfinder/data/${AMRFINDER_DB_VER} && \ + echo "Downloading amrfinder databases and indexing them now..." && \ + wget -q -P /amrfinder/data/${AMRFINDER_DB_VER} ftp://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/4.0/${AMRFINDER_DB_VER}/* && \ + amrfinder_index /amrfinder/data/${AMRFINDER_DB_VER} && \ + ln -s /amrfinder/data/${AMRFINDER_DB_VER} /amrfinder/data/latest + +# set final working directory +WORKDIR /data + +# default command is to print help options +CMD [ "amrfinder", "--help" ] + +## Test stage +FROM app AS test + +# list database version and available --organism options +RUN amrfinder -l + +# run recommended tests from amrfinder; check that stx2a_operon is detected in outputs, meaning stxtyper ran correctly +RUN cd /amrfinder && \ + bash test_amrfinder.sh . && \ + echo && echo "Checking for stx2a_operon string in test outputs..." && \ + grep 'stx2a_operon' test_both.got + +# run amrfinder on Salmonella, without and with --organism option +RUN echo "Downloading Salmeonlla genome (GCA_010941835.1_PDT000052640.3) for testing now..." && \ + 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 && \ + amrfinder --threads 4 --plus --nucleotide GCA_010941835.1_PDT000052640.3_genomic.fna.gz --output test1.txt && \ + amrfinder --threads 4 --plus --nucleotide GCA_010941835.1_PDT000052640.3_genomic.fna.gz --organism Salmonella --output test2.txt && \ + cat test1.txt test2.txt + +# run amrfinder on Klebesiella oxytoca using --organism/-O flag +RUN echo "Downloading Klembsiella oxytoca genome (GCA_003812925.1_ASM381292v1) for testing now..." && \ + wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/812/925/GCA_003812925.1_ASM381292v1/GCA_003812925.1_ASM381292v1_genomic.fna.gz && \ + amrfinder --threads 4 --plus --name GCA_003812925.1 -n GCA_003812925.1_ASM381292v1_genomic.fna.gz -O Klebsiella_oxytoca -o GCA_003812925.1-amrfinder.tsv + +# test that gunzip is installed +RUN gunzip --help diff --git a/ncbi-amrfinderplus/4.0.3-2024-10-22.1/README.md b/ncbi-amrfinderplus/4.0.3-2024-10-22.1/README.md new file mode 100755 index 000000000..dec2e5422 --- /dev/null +++ b/ncbi-amrfinderplus/4.0.3-2024-10-22.1/README.md @@ -0,0 +1,69 @@ +# NCBI AMRFinderPlus docker image + +Main tool : [NCBI AMRFinderPlus](https://github.com/ncbi/amr) + +Additional tools: + +- hmmer v3.3.2 +- ncbi-blast+ v2.16.0 +- [stxtyper](https://github.com/ncbi/stxtyper/) v1.0.27 (Shiga toxin subtyping tool, added in AMRFinderPlus v4.0.3) + +## Database information + +The database included at time of docker image build is **`2024-10-22.1`**. More information can be found in the [changelog.txt on NCBI's FTP](https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/4.0/2024-10-22.1/changes.txt). + +Full documentation: [https://github.com/ncbi/amr/wiki](https://github.com/ncbi/amr/wiki) + +## Docker Image Tags + +Beginning with AMRFinderPlus v3.11.2, we will include the version of AMRFinderPlus followed by the database version in the docker image tag so that it is more informative to users. The format is as follows: + +```bash +# general format +staphb/ncbi-amrfinderplus:- + +# example +staphb/ncbi-amrfinderplus:3.11.14-2023-04-17.1 +``` + +You can view all available docker images on [dockerhub](https://hub.docker.com/r/staphb/ncbi-amrfinderplus/tags) and [quay.io](https://quay.io/repository/staphb/ncbi-amrfinderplus?tab=tags) + +## Example Usage + +```bash +# list out the available organisms for the -O/--organism flag +$ amrfinder -l +Running: amrfinder -l +Software directory: '/amrfinder/' +Software version: 3.12.8 +Database directory: '/amrfinder/data/2024-01-31.1' +Database version: 2024-01-31.1 + +Available --organism options: Acinetobacter_baumannii, Burkholderia_cepacia, Burkholderia_pseudomallei, Campylobacter, +Citrobacter_freundii, Clostridioides_difficile, Enterobacter_asburiae, Enterobacter_cloacae, Enterococcus_faecalis, +Enterococcus_faecium, Escherichia, Klebsiella_oxytoca, Klebsiella_pneumoniae, Neisseria_gonorrhoeae, +Neisseria_meningitidis, Pseudomonas_aeruginosa, Salmonella, Serratia_marcescens, Staphylococcus_aureus, +Staphylococcus_pseudintermedius, Streptococcus_agalactiae, Streptococcus_pneumoniae, Streptococcus_pyogenes, +Vibrio_cholerae, Vibrio_parahaemolyticus, Vibrio_vulnificus + +# download Klebsiella oxytoca genome FASTA/FNA to use as a test +$ wget "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/812/925/GCA_003812925.1_ASM381292v1/GCA_003812925.1_ASM381292v1_genomic.fna.gz" + +# uncompress the FNA file +$ gzip -d GCA_003812925.1_ASM381292v1_genomic.fna.gz + +# run amrfinder (nucleotide mode) on the uncompressed FNA file +$ amrfinder --plus --name GCA_003812925.1 -n GCA_003812925.1_ASM381292v1_genomic.fna -O Klebsiella_oxytoca -o GCA_003812925.1-amrfinder.tsv + +# view output TSV +$ column -t -s $'\t' -n GCA_003812925.1-amrfinder.tsv +Name Protein identifier Contig id Start Stop Strand Gene symbol Sequence name Scope Element type Element subtype Class Subclass Method Target length Reference sequence length % Coverage of reference sequence % Identity to reference sequence Alignment length Accession of closest sequence Name of closest sequence HMM id HMM description +GCA_003812925.1 NA CP033844.1 369234 370406 + oqxA multidrug efflux RND transporter periplasmic adaptor subunit OqxA core AMR AMR PHENICOL/QUINOLONE PHENICOL/QUINOLONE BLASTX 391 391 100.00 90.79 391 WP_002914189.1 multidrug efflux RND transporter periplasmic adaptor subunit OqxA NA NA +GCA_003812925.1 NA CP033844.1 370433 373582 + oqxB multidrug efflux RND transporter permease subunit OqxB core AMR AMR PHENICOL/QUINOLONE PHENICOL/QUINOLONE BLASTX 1050 1050 100.00 96.86 1050 WP_023323140.1 multidrug efflux RND transporter permease subunit OqxB15 NA NA +GCA_003812925.1 NA CP033844.1 636118 637917 - ybtQ yersiniabactin ABC transporter ATP-binding/permease protein YbtQ plus VIRULENCE VIRULENCE NA NA BLASTX 600 600 100.00 89.17 600 AAC69584.1 yersiniabactin ABC transporter ATP-binding/permease protein YbtQ NA NA +GCA_003812925.1 NA CP033844.1 637913 639706 - ybtP yersiniabactin ABC transporter ATP-binding/permease protein YbtP plus VIRULENCE VIRULENCE NA NA BLASTX 598 600 99.67 89.30 598 CAA21388.1 yersiniabactin ABC transporter ATP-binding/permease protein YbtP NA NA +GCA_003812925.1 NA CP033844.1 3473617 3474798 + emrD multidrug efflux MFS transporter EmrD plus AMR AMR EFFLUX EFFLUX BLASTX 394 394 100.00 94.16 394 ACN65732.1 multidrug efflux MFS transporter EmrD NA NA +GCA_003812925.1 NA CP033844.1 5085488 5086357 - blaOXY-2-1 extended-spectrum class A beta-lactamase OXY-2-1 core AMR AMR BETA-LACTAM CEPHALOSPORIN ALLELEX 290 290 100.00 100.00 290 WP_032727905.1 extended-spectrum class A beta-lactamase OXY-2-1 NA NA +GCA_003812925.1 NA CP033845.1 5102 5632 - ant(2'')-Ia aminoglycoside nucleotidyltransferase ANT(2'')-Ia core AMR AMR AMINOGLYCOSIDE GENTAMICIN/KANAMYCIN/TOBRAMYCIN BLASTX 177 177 100.00 98.31 177 WP_000381803.1 aminoglycoside nucleotidyltransferase ANT(2'')-Ia NA NA +GCA_003812925.1 NA CP033846.1 748 1932 - tet(39) tetracycline efflux MFS transporter Tet(39) core AMR AMR TETRACYCLINE TETRACYCLINE EXACTX 395 395 100.00 100.00 395 WP_004856455.1 tetracycline efflux MFS transporter Tet(39) +``` From a2de1b1a60d64c7c5e784b25a058584df7537445 Mon Sep 17 00:00:00 2001 From: Curtis Kapsak Date: Thu, 7 Nov 2024 16:44:17 +0000 Subject: [PATCH 2/5] update main readme --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 60e939df0..1d9235beb 100644 --- a/README.md +++ b/README.md @@ -222,7 +222,7 @@ To learn more about the docker pull rate limits and the open source software pro | [NanoPlot](https://hub.docker.com/r/staphb/nanoplot)
[![docker pulls](https://badgen.net/docker/pulls/staphb/nanoplot)](https://hub.docker.com/r/staphb/nanoplot) |
  • [1.27.0](./nanoplot/1.27.0/)
  • [1.29.0](./nanoplot/1.29.0/)
  • [1.30.1](./nanoplot/1.30.1/)
  • [1.32.0](./nanoplot/1.32.0/)
  • [1.33.0](./nanoplot/1.33.0/)
  • [1.40.0](./nanoplot/1.40.0/)
  • [1.41.6](./nanoplot/1.41.6/)
  • [1.42.0](./nanoplot/1.42.0/)
| https://github.com/wdecoster/NanoPlot | | [ngmaster](https://hub.docker.com/r/staphb/ngmaster)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ngmaster)](https://hub.docker.com/r/staphb/ngmaster) |
  • 0.5.8
  • 1.0.0
| https://github.com/MDU-PHL/ngmaster | | [NCBI Datasets](https://hub.docker.com/r/staphb/ncbi-datasets)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-datasets)](https://hub.docker.com/r/staphb/ncbi-datasets) |
Click to see all datasets versions **datasets versions**
  • [13.31.0](./ncbi-datasets/13.31.0/)
  • [13.35.0](./ncbi-datasets/13.35.0/)
  • [13.43.2](./ncbi-datasets/13.43.2/)
  • [14.0.0](./ncbi-datasets/14.0.0/)
  • [14.3.0](./ncbi-datasets/14.3.0/)
  • [14.7.0](./ncbi-datasets/14.7.0/)
  • [14.13.2](./ncbi-datasets/14.13.2/)
  • [14.20.0](./ncbi-datasets/14.20.0/)
  • [14.27.0](ncbi-datasets/14.27.0/)
  • [15.1.0](ncbi-datasets/15.1.0/)
  • [15.2.0](ncbi-datasets/15.2.0/)
  • [15.11.0](ncbi-datasets/15.11.0/)
  • [15.27.1](ncbi-datasets/15.27.1/)
  • [15.31.0](ncbi-datasets/15.31.1/)
  • [16.2.0](ncbi-datasets/16.2.0/)
  • [16.8.1](./ncbi-datasets/16.8.1/)
  • [16.10.3](./ncbi-datasets/16.10.3/)
  • [16.15.0](./ncbi-datasets/16.15.0/)
  • [16.22.1](./ncbi-datasets/16.22.1/)
  • [16.30.0](./ncbi-datasets/16.30.0/)
| [https://github.com/ncbi/datasets](https://github.com/ncbi/datasets)
[https://www.ncbi.nlm.nih.gov/datasets/docs/v1/](https://www.ncbi.nlm.nih.gov/datasets/docs/v1/) | -| [NCBI AMRFinderPlus](https://hub.docker.com/r/staphb/ncbi-amrfinderplus)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-amrfinderplus)](https://hub.docker.com/r/staphb/ncbi-amrfinderplus) | **AMRFinderPlus & database verion**
Click to see AMRFinderplus v3.11.4 and older versions!
  • 3.1.1b
  • 3.8.4
  • 3.8.28
  • 3.9.3
  • 3.9.8
  • 3.10.1
  • 3.10.5
  • 3.10.16
  • 3.10.20
  • 3.10.24
  • 3.10.30
  • 3.10.36
  • 3.10.42
  • 3.11.2 & 2022-12-19.1
  • [3.11.2 & 2023-02-23.1](ncbi-amrfinderplus/3.11.2-2023-02-23.1/)
  • [3.11.4 & 2023-02-23.1](ncbi-amrfinderplus/3.11.4-2023-02-23.1/)
  • [3.11.8 & 2023-02-23.1](ncbi-amrfinderplus/3.11.8-2023-02-23.1/)
  • [3.11.11 & 2023-04-17.1](ncbi-amrfinderplus/3.11.11-2023-04-17.1)
  • [3.11.14 & 2023-04-17.1](ncbi-amrfinderplus/3.11.14-2023-04-17.1/)
  • [3.11.17 & 2023-07-13.2](ncbi-amrfinderplus/3.11.17-2023-07-13.2/)
  • [3.11.18 & 2023-08-08.2](ncbi-amrfinderplus/3.11.18-2023-08-08.2/)
  • [3.11.20 & 2023-09-26.1](ncbi-amrfinderplus/3.11.20-2023-09-26.1/)
  • [3.11.26 & 2023-11-15.1](ncbi-amrfinderplus/3.11.26-2023-11-15.1/)
  • [3.12.8 & 2024-01-31.1](ncbi-amrfinderplus/3.12.8-2024-01-31.1/)
  • [3.12.8 & 2024-05-02.2](./ncbi-amrfinderplus/3.12.8-2024-05-02.2/)
  • [3.12.8 & 2024-07-22.1](./ncbi-amrfinderplus/3.12.8-2024-07-22.1/)
| [https://github.com/ncbi/amr](https://github.com/ncbi/amr) | +| [NCBI AMRFinderPlus](https://hub.docker.com/r/staphb/ncbi-amrfinderplus)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-amrfinderplus)](https://hub.docker.com/r/staphb/ncbi-amrfinderplus) | **AMRFinderPlus & database verion**
Click to see AMRFinderplus v3.11.4 and older versions!
  • 3.1.1b
  • 3.8.4
  • 3.8.28
  • 3.9.3
  • 3.9.8
  • 3.10.1
  • 3.10.5
  • 3.10.16
  • 3.10.20
  • 3.10.24
  • 3.10.30
  • 3.10.36
  • 3.10.42
  • 3.11.2 & 2022-12-19.1
  • [3.11.2 & 2023-02-23.1](ncbi-amrfinderplus/3.11.2-2023-02-23.1/)
  • [3.11.4 & 2023-02-23.1](ncbi-amrfinderplus/3.11.4-2023-02-23.1/)
  • [3.11.8 & 2023-02-23.1](ncbi-amrfinderplus/3.11.8-2023-02-23.1/)
  • [3.11.11 & 2023-04-17.1](ncbi-amrfinderplus/3.11.11-2023-04-17.1)
  • [3.11.14 & 2023-04-17.1](ncbi-amrfinderplus/3.11.14-2023-04-17.1/)
  • [3.11.17 & 2023-07-13.2](ncbi-amrfinderplus/3.11.17-2023-07-13.2/)
  • [3.11.18 & 2023-08-08.2](ncbi-amrfinderplus/3.11.18-2023-08-08.2/)
  • [3.11.20 & 2023-09-26.1](ncbi-amrfinderplus/3.11.20-2023-09-26.1/)
  • [3.11.26 & 2023-11-15.1](ncbi-amrfinderplus/3.11.26-2023-11-15.1/)
  • [3.12.8 & 2024-01-31.1](ncbi-amrfinderplus/3.12.8-2024-01-31.1/)
  • [3.12.8 & 2024-05-02.2](./ncbi-amrfinderplus/3.12.8-2024-05-02.2/)
  • [3.12.8 & 2024-07-22.1](./ncbi-amrfinderplus/3.12.8-2024-07-22.1/)
  • [4.0.3 & 2024-10-22.1 (includes stxtyper)](./ncbi-amrfinderplus/4.0.3-2024-10-22.1/)
| [https://github.com/ncbi/amr](https://github.com/ncbi/amr) | | [NCBI table2asn](https://hub.docker.com/r/staphb/ncbi-table2asn)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-table2asn)](https://hub.docker.com/r/staphb/ncbi-table2asn) |
  • [1.26.678](./ncbi-table2asn/1.26.678/)
  • [1.28.943](./ncbi-table2asn/1.28.943/)
  • [1.28.1021](./ncbi-table2asn/1021/)
| [https://www.ncbi.nlm.nih.gov/genbank/table2asn/](https://www.ncbi.nlm.nih.gov/genbank/table2asn/)
[https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/](https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/) | | [ONTime](https://hub.docker.com/r/staphb/ontime)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ontime)](https://hub.docker.com/r/staphb/ontime) |
  • [0.2.3](ontime/0.2.3/)
  • [0.3.1](ontime/0.3.1/)
| https://github.com/mbhall88/ontime | | [OrthoFinder](https://hub.docker.com/r/staphb/orthofinder)
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  • 2.17
| https://github.com/davidemms/OrthoFinder | From 2c4468fe6329026bc95c7d5ab428c71fb759ab0e Mon Sep 17 00:00:00 2001 From: Curtis Kapsak Date: Thu, 7 Nov 2024 16:49:07 +0000 Subject: [PATCH 3/5] fix typos --- ncbi-amrfinderplus/4.0.3-2024-10-22.1/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ncbi-amrfinderplus/4.0.3-2024-10-22.1/Dockerfile b/ncbi-amrfinderplus/4.0.3-2024-10-22.1/Dockerfile index 49e9facfb..4e63aa914 100755 --- a/ncbi-amrfinderplus/4.0.3-2024-10-22.1/Dockerfile +++ b/ncbi-amrfinderplus/4.0.3-2024-10-22.1/Dockerfile @@ -85,14 +85,14 @@ RUN cd /amrfinder && \ grep 'stx2a_operon' test_both.got # run amrfinder on Salmonella, without and with --organism option -RUN echo "Downloading Salmeonlla genome (GCA_010941835.1_PDT000052640.3) for testing now..." && \ +RUN echo "Downloading Salmonella genome (GCA_010941835.1_PDT000052640.3) for testing now..." && \ 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 && \ amrfinder --threads 4 --plus --nucleotide GCA_010941835.1_PDT000052640.3_genomic.fna.gz --output test1.txt && \ amrfinder --threads 4 --plus --nucleotide GCA_010941835.1_PDT000052640.3_genomic.fna.gz --organism Salmonella --output test2.txt && \ cat test1.txt test2.txt # run amrfinder on Klebesiella oxytoca using --organism/-O flag -RUN echo "Downloading Klembsiella oxytoca genome (GCA_003812925.1_ASM381292v1) for testing now..." && \ +RUN echo "Downloading Klebsiella oxytoca genome (GCA_003812925.1_ASM381292v1) for testing now..." && \ wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/812/925/GCA_003812925.1_ASM381292v1/GCA_003812925.1_ASM381292v1_genomic.fna.gz && \ amrfinder --threads 4 --plus --name GCA_003812925.1 -n GCA_003812925.1_ASM381292v1_genomic.fna.gz -O Klebsiella_oxytoca -o GCA_003812925.1-amrfinder.tsv From ee662289b38ed29349cc06dfbe32e1e21ae5d7fa Mon Sep 17 00:00:00 2001 From: Young Date: Thu, 7 Nov 2024 12:26:45 -0700 Subject: [PATCH 4/5] Changed cat to head for better result deliniation --- ncbi-amrfinderplus/4.0.3-2024-10-22.1/Dockerfile | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/ncbi-amrfinderplus/4.0.3-2024-10-22.1/Dockerfile b/ncbi-amrfinderplus/4.0.3-2024-10-22.1/Dockerfile index 4e63aa914..5604c3ea4 100755 --- a/ncbi-amrfinderplus/4.0.3-2024-10-22.1/Dockerfile +++ b/ncbi-amrfinderplus/4.0.3-2024-10-22.1/Dockerfile @@ -89,12 +89,13 @@ RUN echo "Downloading Salmonella genome (GCA_010941835.1_PDT000052640.3) for tes 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 && \ amrfinder --threads 4 --plus --nucleotide GCA_010941835.1_PDT000052640.3_genomic.fna.gz --output test1.txt && \ amrfinder --threads 4 --plus --nucleotide GCA_010941835.1_PDT000052640.3_genomic.fna.gz --organism Salmonella --output test2.txt && \ - cat test1.txt test2.txt + head test1.txt test2.txt # run amrfinder on Klebesiella oxytoca using --organism/-O flag RUN echo "Downloading Klebsiella oxytoca genome (GCA_003812925.1_ASM381292v1) for testing now..." && \ wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/812/925/GCA_003812925.1_ASM381292v1/GCA_003812925.1_ASM381292v1_genomic.fna.gz && \ - amrfinder --threads 4 --plus --name GCA_003812925.1 -n GCA_003812925.1_ASM381292v1_genomic.fna.gz -O Klebsiella_oxytoca -o GCA_003812925.1-amrfinder.tsv + amrfinder --threads 4 --plus --name GCA_003812925.1 -n GCA_003812925.1_ASM381292v1_genomic.fna.gz -O Klebsiella_oxytoca -o GCA_003812925.1-amrfinder.tsv & \ + head GCA_003812925.1-amrfinder.tsv # test that gunzip is installed RUN gunzip --help From fda6f99c61351a55b7538efa905ef668b846cd60 Mon Sep 17 00:00:00 2001 From: Young Date: Thu, 7 Nov 2024 12:33:33 -0700 Subject: [PATCH 5/5] fixed typo --- ncbi-amrfinderplus/4.0.3-2024-10-22.1/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ncbi-amrfinderplus/4.0.3-2024-10-22.1/Dockerfile b/ncbi-amrfinderplus/4.0.3-2024-10-22.1/Dockerfile index 5604c3ea4..33b978e10 100755 --- a/ncbi-amrfinderplus/4.0.3-2024-10-22.1/Dockerfile +++ b/ncbi-amrfinderplus/4.0.3-2024-10-22.1/Dockerfile @@ -94,7 +94,7 @@ RUN echo "Downloading Salmonella genome (GCA_010941835.1_PDT000052640.3) for tes # run amrfinder on Klebesiella oxytoca using --organism/-O flag RUN echo "Downloading Klebsiella oxytoca genome (GCA_003812925.1_ASM381292v1) for testing now..." && \ wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/812/925/GCA_003812925.1_ASM381292v1/GCA_003812925.1_ASM381292v1_genomic.fna.gz && \ - amrfinder --threads 4 --plus --name GCA_003812925.1 -n GCA_003812925.1_ASM381292v1_genomic.fna.gz -O Klebsiella_oxytoca -o GCA_003812925.1-amrfinder.tsv & \ + amrfinder --threads 4 --plus --name GCA_003812925.1 -n GCA_003812925.1_ASM381292v1_genomic.fna.gz -O Klebsiella_oxytoca -o GCA_003812925.1-amrfinder.tsv && \ head GCA_003812925.1-amrfinder.tsv # test that gunzip is installed