Kaptive version 2.0.8

README.md

@@ -171,7 +171,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [IRMA](https://hub.docker.com/r/staphb/irma/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/irma)](https://hub.docker.com/r/staphb/irma) | <ul><li>1.0.2</li><li>1.0.3</li><li>1.1.2</li><li>1.1.3</li></ul> | https://wonder.cdc.gov/amd/flu/irma/|
 | [isPcr](https://users.soe.ucsc.edu/~kent/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ispcr)](https://hub.docker.com/r/staphb/ispcr) | <ul><li>[33](ispcr/33/)</li></ul> | https://users.soe.ucsc.edu/~kent/ |
 | [iVar](https://hub.docker.com/r/staphb/ivar/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ivar)](https://hub.docker.com/r/staphb/ivar) | <ul><li>1.1</li><li>1.1 (+SARS-CoV2 reference)</li><li>1.2.1</li><li>1.2.1 (+SC2 ref)</li><li>1.2.2 (+SC2 ref and artic bedfiles)</li><li>1.3</li><li>1.3.1</li><li>1.3.2</li><li>1.4.1</li><li>1.4.2</li></ul> | https://github.com/andersen-lab/ivar |
-| [Kaptive](https://hub.docker.com/r/staphb/kaptive/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kaptive)](https://hub.docker.com/r/staphb/kaptive) | <ul><li>2.0.0</li><li>2.0.3</li><li>2.0.5</li></ul> | https://github.com/katholt/Kaptive/ |
+| [Kaptive](https://hub.docker.com/r/staphb/kaptive/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kaptive)](https://hub.docker.com/r/staphb/kaptive) | <ul><li>[2.0.0](./kaptive/2.0.0/)</li><li>[2.0.3](./kaptive/2.0.3/)</li><li>[2.0.5](./kaptive/2.0.5/)</li><li>[2.0.8](./kaptive/2.0.8/)</li></ul> | https://github.com/klebgenomics/Kaptive |
 | [Kleborate](https://hub.docker.com/r/staphb/kleborate/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kleborate)](https://hub.docker.com/r/staphb/kleborate) | <ul><li>[2.0.4](./kleborate/2.0.4/)</li><li>[2.1.0](./kleborate/2.1.0/)</li><li>[2.2.0](./kleborate/2.3.2/)</li><li>[2.3.2](./kleborate/2.3.2)</li><li>[2.3.2-2023-05](kleborate/2.3.2-2023-05/)</li><li>[2.4.1](kleborate/2.4.1/)</li></ul> | https://github.com/katholt/Kleborate/ <br/> https://github.com/katholt/Kaptive/ |
 | [kma](https://hub.docker.com/r/staphb/kma/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kma)](https://hub.docker.com/r/staphb/kma) | <ul><li>1.2.21</li><li>1.4.10 (no database)</li></ul> | https://bitbucket.org/genomicepidemiology/kma/ |
 | [Kraken](https://hub.docker.com/r/staphb/kraken/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kraken)](https://hub.docker.com/r/staphb/kraken) | <ul><li>1.0</li><li>1.1.1</li><li>1.1.1 (no database)</li></ul> | https://github.com/DerrickWood/kraken |

kaptive/2.0.8/Dockerfile

@@ -0,0 +1,111 @@
+FROM ubuntu:jammy as app
+
+ARG KAPTIVE_VER="2.0.8"
+# note: blast version 2.15 causes errors
+ARG blastVer="2.3.0"
+ARG VP_GENOMOSEROTYPING_VER="1.0"
+# so that apt doesn't try to ask for user input
+ARG BIOPYTHON_VER="1.81"
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="Kaptive"
+LABEL software.version="${KAPTIVE_VER}"
+LABEL description="Report information about surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genome assemblies"
+LABEL website="https://github.com/klebgenomics/Kaptive/"
+LABEL license="https://github.com/klebgenomics/Kaptive/blob/master/LICENSE"
+LABEL website.VPdatabase="https://github.com/aldertzomer/vibrio_parahaemolyticus_genomoserotyping"
+LABEL license.VPdatabase="https://github.com/aldertzomer/vibrio_parahaemolyticus_genomoserotyping/blob/main/LICENSE"
+LABEL maintainer="Tamas Stirling"
+LABEL maintainer.email="[email protected]"
+LABEL maintainer2="Curtis Kapsak"
+LABEL maintainer2.email="[email protected]"
+LABEL maintainer3="Erin Young"
+LABEL maintainer3.email="[email protected]"
+
+# install some dependencies via apt; cleanup apt garbage
+RUN apt-get update && apt-get install -y --no-install-recommends \
+  locales \
+  python3 \
+  python3-pip \
+  python3-setuptools \
+  software-properties-common \
+  wget \
+  ca-certificates \
+  procps \
+  unzip && \
+  rm -rf /var/lib/apt/lists/* && apt-get autoclean
+
+# set locale
+RUN locale-gen en_US.UTF-8 && update-locale LANG=en_US.UTF-8
+ENV LANG=en_US.UTF-8
+
+# ncbi-blast+
+RUN wget -q ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${blastVer}/ncbi-blast-${blastVer}+-x64-linux.tar.gz && \
+  tar -zxpf ncbi-blast-${blastVer}+-x64-linux.tar.gz && \
+  rm -v ncbi-blast-${blastVer}+-x64-linux.tar.gz
+
+# kaptive
+RUN wget -q https://github.com/klebgenomics/Kaptive/archive/refs/tags/v${KAPTIVE_VER}.tar.gz && \
+  tar -xzf v${KAPTIVE_VER}.tar.gz && \
+  rm -vf v${KAPTIVE_VER}.tar.gz && \
+  mv -v /Kaptive-${KAPTIVE_VER} /kaptive
+
+# install biopython globally via system pip
+RUN pip3 install biopython==${BIOPYTHON_VER}
+
+# download Vibrio parahemolyticus database; rename directory to static location
+RUN wget -q https://github.com/aldertzomer/vibrio_parahaemolyticus_genomoserotyping/archive/refs/tags/${VP_GENOMOSEROTYPING_VER}.tar.gz && \
+  tar -xzf ${VP_GENOMOSEROTYPING_VER}.tar.gz && \
+  rm -v ${VP_GENOMOSEROTYPING_VER}.tar.gz && \
+  mv -v vibrio_parahaemolyticus_genomoserotyping-${VP_GENOMOSEROTYPING_VER}/*gbk /kaptive/reference_database/. && \
+  rm -rf vibrio_parahaemolyticus_genomoserotyping-${VP_GENOMOSEROTYPING_VER}
+
+# set $PATH, with /kaptive at the highest priority
+ENV PATH="/kaptive:/ncbi-blast-${blastVer}+/bin:${PATH}"
+
+# final working directory is /data
+WORKDIR /data
+
+# default command is to print help options
+CMD [ "kaptive.py", "--help"]
+
+# test layer
+FROM app as test
+
+WORKDIR /test1
+
+# test with A. baumannii; testing both k and o locus
+RUN echo "downloading an A. baumannii genome & testing Kaptive..." && \
+  wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/016/486/705/GCA_016486705.1_PDT000751301.1/GCA_016486705.1_PDT000751301.1_genomic.fna.gz && \
+  gzip -d GCA_016486705.1_PDT000751301.1_genomic.fna.gz && \
+  kaptive.py -a GCA_016486705.1_PDT000751301.1_genomic.fna -k /kaptive/reference_database/Acinetobacter_baumannii_k_locus_primary_reference.gbk  -o /test1/Abaum && \
+  kaptive.py -a GCA_016486705.1_PDT000751301.1_genomic.fna -k /kaptive/reference_database/Acinetobacter_baumannii_OC_locus_primary_reference.gbk -o /test1/Abaum
+
+WORKDIR /test2
+
+# test with K. pneumoniae; testing both k and o locus
+RUN echo "downloading an K. pneumoniae genome & testing Kaptive..." && \
+  wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/022/268/055/GCA_022268055.1_PDT000434809.1/GCA_022268055.1_PDT000434809.1_genomic.fna.gz && \
+  gzip -d GCA_022268055.1_PDT000434809.1_genomic.fna.gz && \
+  kaptive.py -a GCA_022268055.1_PDT000434809.1_genomic.fna -k /kaptive/reference_database/Klebsiella_k_locus_primary_reference.gbk -o /test2/kpneu && \
+  kaptive.py -a GCA_022268055.1_PDT000434809.1_genomic.fna -k /kaptive/reference_database/Klebsiella_o_locus_primary_reference.gbk -o /test2/kpneu
+
+WORKDIR /test3
+
+### test with at 2 Vibrio parahaemolyticus genomes with a known serotype. These 2 are pulled from the publication describing custom database ##
+# GCA_001558495.2 - expect OL1 and KL1
+# GCA_001728135.1 - expect OL4 KL53
+# more info on test genome here: https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_001558495.2/
+# strain: ATCC17802
+# more info on 2nd test genome here: https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_001728135.1/
+# strain: CDC_K5009W
+RUN echo "downloading an 2 V. parahaemolyticus genomes & testing Kaptive..." && \
+  wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/558/495/GCF_001558495.2_ASM155849v2/GCF_001558495.2_ASM155849v2_genomic.fna.gz && \
+  wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/728/135/GCF_001728135.1_ASM172813v1/GCF_001728135.1_ASM172813v1_genomic.fna.gz && \
+  gzip -d GCF_001558495.2_ASM155849v2_genomic.fna.gz && \
+  gzip -d GCF_001728135.1_ASM172813v1_genomic.fna.gz && \
+  kaptive.py -a *.fna -k /kaptive/reference_database/VibrioPara_Kaptivedb_K.gbk -o /test3/Vparahaemolyticus && \
+  kaptive.py -a *.fna -k /kaptive/reference_database/VibrioPara_Kaptivedb_O.gbk -o /test3/Vparahaemolyticus

kaptive/2.0.8/README.md

@@ -0,0 +1,58 @@
+# Kaptive
+
+Main tool: [Kaptive](https://github.com/klebgenomics/Kaptive)
+
+Additional tools:
+
+- ncbi-blast+ 2.3.0
+- python 3.8.10
+- biopython 1.81
+
+## Kaptive databases
+
+There are few databases included in this docker image for Kaptive v2.0.8:
+
+- Klebsiella pneumoniae species complex
+  - included w/ Kaptive
+- Acinetobacter baumannii
+  - included w/ Kaptive
+- Vibrio parahaemolyticus
+  - Located in separate GitHub repo: https://github.com/aldertzomer/vibrio_parahaemolyticus_genomoserotyping
+  - Publication: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001007
+
+The databases (Genbank/GBK files) are located as follows in the container filesystem:
+
+```bash
+# Klebsiella pneumoniae species complex
+/kaptive/reference_database/Klebsiella_k_locus_primary_reference.gbk
+/kaptive/reference_database/Klebsiella_o_locus_primary_reference.gbk
+
+# Acinetobacter baumannii
+/kaptive/reference_database/Acinetobacter_baumannii_k_locus_primary_reference.gbk
+/kaptive/reference_database/Acinetobacter_baumannii_OC_locus_primary_reference.gbk
+
+# Vibrio parahaeolyticus
+/kaptive/reference_database/VibrioPara_Kaptivedb_K.gbk
+/kaptive/reference_database/VibrioPara_Kaptivedb_O.gbk
+```
+
+Example commands for each of these databases can be found below.
+
+## Example Usage
+
+```bash
+# K locus, A. baumannii
+kaptive.py -a assembly.fasta -k /kaptive/reference_database/Acinetobacter_baumannii_k_locus_primary_reference.gbk
+# O locus, A. baumannii
+kaptive.py -a assembly.fasta -k /kaptive/reference_database/Acinetobacter_baumannii_OC_locus_primary_reference.gbk
+
+# K locus, K. pneumoniae
+kaptive.py -a assembly.fasta -k /kaptive/reference_database/Klebsiella_k_locus_primary_reference.gbk
+# O locus, K. pneumoniae
+kaptive.py -a assembly.fasta -k /kaptive/reference_database/Klebsiella_o_locus_primary_reference.gbk
+
+# K locus, V. parahaemolyticus
+kaptive.py -a assembly.fasta -k /kaptive/reference_database/VibrioPara_Kaptivedb_K.gbk
+# O locus, V. parahaemolyticus
+kaptive.py -a assembly.fasta -k /kaptive/reference_database/VibrioPara_Kaptivedb_O.gbk
+```