StaPH-B · erinyoung · Feb 24, 2025 · Feb 24, 2025 · Feb 26, 2025
diff --git a/README.md b/README.md
@@ -278,7 +278,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [RAxML](https://hub.docker.com/r/staphb/raxml/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/raxml)](https://hub.docker.com/r/staphb/raxml) | <ul><li>8.2.12</li><li>[8.2.13](./raxml/8.2.13/)</li></ul> | https://github.com/stamatak/standard-RAxML |
 | [RAxML-NG](https://hub.docker.com/r/staphb/raxml-ng/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/raxml-ng)](https://hub.docker.com/r/staphb/raxml-ng) | <ul><li>[1.2.2](./raxml-ng/1.2.2/)</li></ul> | https://github.com/amkozlov/raxml-ng |
 | [rdp](https://hub.docker.com/r/staphb/rdp) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/rdp)](https://hub.docker.com/r/staphb/rdp) | <ul><li>[2.14](./rdp/0.4.0/)</li></ul> | https://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.14.zip/download |
-| [ResFinder](https://hub.docker.com/r/staphb/resfinder/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/resfinder)](https://hub.docker.com/r/staphb/resfinder) | <ul><li>[4.1.1](./resfinder/4.1.11/)</li><li>[4.5.0](./resfinder/4.5.0/)</li></ul> | https://bitbucket.org/genomicepidemiology/resfinder/src/master/ |
+| [ResFinder](https://hub.docker.com/r/staphb/resfinder/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/resfinder)](https://hub.docker.com/r/staphb/resfinder) | <ul><li>[4.1.1](./build-files/resfinder/4.1.11/)</li><li>[4.5.0](./build-files/resfinder/4.5.0/)</li><li>[4.6.0](./build-files/resfinder/4.6.0/)</li></ul> | https://bitbucket.org/genomicepidemiology/resfinder/src/master/ |
 | [Roary](https://hub.docker.com/r/staphb/roary/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/roary)](https://hub.docker.com/r/staphb/roary) | <ul><li>3.12.0</li><li>3.13.0</li></ul> | https://github.com/sanger-pathogens/Roary |
 | [SalmID](https://hub.docker.com/r/staphb/salmid) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/salmid)](https://hub.docker.com/r/staphb/salmid) | <ul><li>0.1.23</li></ul> | https://github.com/hcdenbakker/SalmID |
 | [samclip](https://hub.docker.com/r/staphb/samclip) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/samclip)](https://hub.docker.com/r/staphb/samclip) | <ul><li>[0.4.0](./samclip/0.4.0/)</li></ul>| https://github.com/tseemann/samclip |

diff --git a/build-files/resfinder/4.6.0/Dockerfile b/build-files/resfinder/4.6.0/Dockerfile
@@ -0,0 +1,164 @@
+ARG RESFINDER_VER="4.6.0"
+
+FROM ubuntu:jammy AS app
+
+# ARG sets environment variables during the build stage
+ARG RESFINDER_VER
+ARG KMA_VER="1.4.18"
+
+# Database may not be properly versioned, but using a version tag here (2024-08-06)
+# see here: https://bitbucket.org/genomicepidemiology/resfinder_db/downloads/?tab=tags
+ARG RESFINDER_DB_COMMIT_HASH="2.4.0"
+
+# Database may not be properly versioned, but using a version tag here (2024-08-08)
+# see here: https://bitbucket.org/genomicepidemiology/pointfinder_db/downloads/?tab=tags
+ARG POINTFINDER_DB_COMMIT_HASH="4.1.1"
+
+# Database may not be properly versioned, but using a version tag here (2023-05-31)
+# see here: https://bitbucket.org/genomicepidemiology/disinfinder_db/downloads/?tab=tags
+ARG DISINFINDER_DB_COMMIT_HASH="2.0.1"
+
+# LABEL instructions tag the image with metadata that might be important to the user
+# Optional, but highly recommended
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="resfinder"
+LABEL software.version=${RESFINDER_VER}
+LABEL description="Identifies acquired resistance genes and point mutations in total or partial sequenced isolates of bacteria."
+LABEL website="https://bitbucket.org/genomicepidemiology/resfinder/src/master/"
+LABEL license="https://bitbucket.org/genomicepidemiology/resfinder/src/master/README.md"
+LABEL maintainer="Curtis Kapsak"
+LABEL maintainer.email="kapsakcj@gmail.com"
+
+# so that apt doesn't ask for a region during apt install step
+ARG DEBIAN_FRONTEND noninteractive
+
+# install dependencies; cleanup apt garbage 
+# ncbi-blast+ 2.12.0+ds-3build1 (ubuntu:jammy)
+# python3 v3.10
+RUN apt-get update && apt-get install -y --no-install-recommends \
+  wget \
+  ca-certificates \
+  procps \
+  git \
+  ncbi-blast+ \
+  python3 \
+  python3-pip \
+  python3-setuptools \
+  python3-dev \
+  gcc \
+  make \
+  libz-dev \
+  unzip && \
+  apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# Install resfinder ()
+# It is no longer recommended to clone the ResFinder bitbucket repository unless you plan to do development work on ResFinder.
+# Instead we recommend installing ResFinder using pip...
+# https://bitbucket.org/genomicepidemiology/resfinder/src/master/ 2024-03-21
+RUN pip3 install --no-cache-dir resfinder==${RESFINDER_VER} && \
+  mkdir /data
+
+# Install kma
+RUN git clone --branch ${KMA_VER} --depth 1 https://bitbucket.org/genomicepidemiology/kma.git && \
+  cd kma && \
+  make && \
+  mv -v kma* /usr/local/bin/
+
+# pointfinder database install
+RUN mkdir /pointfinder_db && \
+  git clone --branch ${POINTFINDER_DB_COMMIT_HASH} --depth 1 https://git@bitbucket.org/genomicepidemiology/pointfinder_db.git /pointfinder_db && \
+  cd /pointfinder_db && \
+  python3 INSTALL.py /usr/local/bin/kma_index non_interactive
+
+# resfinder database install
+RUN mkdir /resfinder_db && \
+  git clone --branch ${RESFINDER_DB_COMMIT_HASH} --depth 1 https://git@bitbucket.org/genomicepidemiology/resfinder_db.git /resfinder_db && \
+  cd /resfinder_db && \
+  python3 INSTALL.py /usr/local/bin/kma_index non_interactive
+
+# disinfinder database install
+RUN mkdir /disinfinder_db && \
+  git clone --branch ${DISINFINDER_DB_COMMIT_HASH} --depth 1 https://git@bitbucket.org/genomicepidemiology/disinfinder_db.git /disinfinder_db && \
+  cd /disinfinder_db && \
+  python3 INSTALL.py /usr/local/bin/kma_index non_interactive
+
+# so that run_resfinder.py is in the PATH
+ENV PATH="${PATH}" \
+  # specifying database locations
+  CGE_RESFINDER_RESGENE_DB="/resfinder_db" \
+  CGE_RESFINDER_RESPOINT_DB="/pointfinder_db" \
+  CGE_DISINFINDER_DB="/disinfinder_db"
+
+# setting a janky alias for everyone that uses the "latest" tag 
+RUN echo -e '#!/bin/bash\npython3 -m resfinder "$@"' > /usr/bin/run_resfinder.py && \
+    chmod +x /usr/bin/run_resfinder.py
+
+CMD python3 -m resfinder -h
+
+WORKDIR /data
+
+FROM app AS test
+
+ARG RESFINDER_VER
+
+# checking suggested usage and alias
+RUN python3 -m resfinder -h && run_resfinder.py --help
+
+WORKDIR /test
+
+# getting test files
+RUN git clone --branch ${RESFINDER_VER} --depth 1 https://git@bitbucket.org/genomicepidemiology/resfinder.git 
+
+##### short description of included test files #####
+### test files for typical gene detection (or lack thereof)
+# test_isolate_01.fa fasta header ">test_isolate_01 blaB-2_1_AF189300"
+# test_isolate_02.fa fasta header ">test_isolate_02 blaCTX-M-33_1_AY238472"
+# test_isolate_03.fa fasta header ">test_isolate_03 no_res"
+
+### test FASTA files for point mutation detection
+# test_isolate_05.fa fasta header ">test_isolate_05 gyrA_mut
+# test_isolate_09a.fa fasta header ">gyrA_G81D_GGT241GAT"
+# test_isolate_09b.fa fasta header ">gyrA_G81D_GAT_D82G_GGC"
+
+# test fastq files are also available for isolates 01, 05, 09a, and 09b. They are used to test KMA's functionality
+
+# run resfinder on supplied fasta files for gene detection (-acq for acquired genes, NOT point mutations)
+RUN echo "TESTING RESFINDER ON SUPPLIED FASTA FILES FOR ACQUIRED GENES" && \
+  for ISOLATE in 01 02 03; do \
+    python3 -m resfinder -ifa /test/resfinder/tests/data/test_isolate_${ISOLATE}.fa -o test_resfinder_fastaInput_isolate_${ISOLATE} -acq -l 0.9 -t 0.9; \
+  done && \
+  ls test_resfinder_fastaInput_*
+
+# run resfinder on supplied fastq files for gene detection (-acq for acquired genes, and -c -s "Escherichia coli" for point mutations)
+RUN echo "TESTING RESFINDER ON SUPPLIED FASTQ FILES FOR ACQUIRED GENES AND POINT MUTATIONS" && \
+  for ISOLATE in 01 05 09a 09b ; do \
+    python3 -m resfinder -ifq /test/resfinder/tests/data/test_isolate_${ISOLATE}_1.fq /test/resfinder/tests/data/test_isolate_${ISOLATE}_2.fq \
+      -o test_resfinder_fastqInput_isolate_${ISOLATE} \
+      -acq -l 0.9 -t 0.9\
+      -c -s "Escherichia coli"; \
+  done && \
+  ls test_resfinder_fastqInput_*
+
+# run resfinder on supplied fasta files for point mutation detection (-c and --species for point mutations, NOT acquired resistance genes)
+RUN echo "TESTING RESFINDER ON SUPPLIED FASTA FILES FOR POINT MUTAITON DETECTION" && \
+  for ISOLATE in 05 09a 09b ; do \
+    python3 -m resfinder -ifa /test/resfinder/tests/data/test_isolate_${ISOLATE}.fa -o test_pointfinder_fastaInput_isolate_${ISOLATE} -c --species "Escherichia coli"; \
+  done && \
+  ls test_pointfinder*
+
+# look for expected outputs in resulting files; grep exits 1 if term is not found, meaning test layer will not build properly
+RUN echo "FASTA INPUTS, SEARCHING FOR EXPECTED (RESFINDER) OUTPUTS:" && \
+  grep 'blaB-2' test_resfinder_fastaInput_isolate_01/ResFinder_results_tab.txt && \
+  grep 'blaCTX' test_resfinder_fastaInput_isolate_02/ResFinder_results_tab.txt && \
+  grep -B 1 'No hit found' test_resfinder_fastaInput_isolate_03/ResFinder_results_table.txt && \
+  echo "FASTQ INPUT TESTS, SEARCHING FOR EXPECTED (POINTFINDER AND RESFINDER) OUTPUTS:" && \
+  grep "blaB-2" test_resfinder_fastqInput_isolate_01/ResFinder_results_tab.txt && \
+  grep "gyrA p.S83A" test_resfinder_fastqInput_isolate_05/PointFinder_table.txt && \
+  grep "gyrA p.G81D" test_resfinder_fastqInput_isolate_09a/PointFinder_table.txt && \
+  grep "gyrA p.G81D" test_resfinder_fastqInput_isolate_09b/PointFinder_table.txt && \
+  echo "FASTA INPUTS, SEARCHING FOR EXPECTED (POINTFINDER) OUTPUTS:" && \
+  grep "gyrA p.S83A" test_pointfinder_fastaInput_isolate_05/PointFinder_table.txt && \
+  grep "gyrA p.G81D" test_pointfinder_fastaInput_isolate_09a/PointFinder_table.txt && \
+  grep "gyrA p.G81D" test_pointfinder_fastaInput_isolate_09b/PointFinder_table.txt && \
+  grep "gyrA p.D82G" test_pointfinder_fastaInput_isolate_09b/PointFinder_table.txt
diff --git a/build-files/resfinder/4.6.0/README.md b/build-files/resfinder/4.6.0/README.md
@@ -0,0 +1,35 @@
+# ResFinder container
+
+Main tool : [ResFinder](https://bitbucket.org/genomicepidemiology/resfinder/src/master/)
+
+Additional tools:
+
+- kma 1.4.17
+- ResFinder database 2.4.0
+- PointFinder database 4.1.1
+- DisinFinder database 2.0.1
+
+Alternatively available as a webtool here: https://cge.cbs.dtu.dk/services/ResFinder/
+
+Full documentation: https://bitbucket.org/genomicepidemiology/resfinder/src/master/
+
+ResFinder identifies acquired genes and/or finds chromosomal mutations mediating antimicrobial resistance in total or partial DNA sequence of bacteria.
+
+WARNING : The executable has changed!
+
+## Example Usage
+
+```bash
+# run ResFinder on raw reads (FASTQs)
+python3 -m resfinder -ifq /data/sample_1.fastq /data/sample_2.fastq \
+    -o /data/resfinder-results-fastq-input \
+    -acq -l 0.9 -t 0.9 \
+    -c -s "Escherichia coli"
+
+# run ResFinder on assembly FASTA
+python3 -m resfinder -ifa /data/sample.fasta \
+    -o /data/resfinder-results-fasta-input \
+    -c \
+    -acq -l 0.9 -t 0.9 \
+    --species "Escherichia coli" \
+```