adding cat_pack version 6.0.1

Program_Licenses.md

@@ -27,7 +27,7 @@ The licenses of the open-source software that is contained in these Docker image
 | BUSCO | MIT | https://gitlab.com/ezlab/busco/-/raw/master/LICENSE |
 | BWA | GNU GPLv3 | https://github.com/lh3/bwa/blob/master/COPYING |
 | Canu <br/> Racon <br/> Minimap2 | GNU GPLv3 (Canu), <br/> MIT (Racon), <br/> MIT (Minimap2) | https://github.com/marbl/canu/blob/master/README.license.GPL https://github.com/isovic/racon/blob/master/LICENSE https://github.com/lh3/minimap2/blob/master/LICENSE.txt |
-| CAT | MIT | https://github.com/MGXlab/CAT_pack?tab=MIT-1-ov-file#readme |
+| CAT | MIT | https://github.com/MGXlab/CAT_pack?tab=MIT-1-ov-file#readme and https://github.com/MGXlab/CAT_pack/blob/master/LICENSE.md |
 | centroid | GitHub No License | https://github.com/https://github.com/stjacqrm/centroid |
 | CDC-SPN | GitHub No License | https://github.com/BenJamesMetcalf/Spn_Scripts_Reference |
 | cfsan-snp-pipeline | non-standard license see --> | https://github.com/CFSAN-Biostatistics/snp-pipeline/blob/master/LICENSE.txt |

README.md

@@ -135,7 +135,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [BWA](https://hub.docker.com/r/staphb/bwa) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bwa)](https://hub.docker.com/r/staphb/bwa) | <ul><li>0.7.17</li><li>[0.7.18](./bwa/0.7.18/)</li></ul> | https://github.com/lh3/bwa |
 | [Canu](https://hub.docker.com/r/staphb/canu) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/canu?)](https://hub.docker.com/r/staphb/canu)| <ul><li>2.0</li><li>2.1.1</li><li>2.2</li></ul> | https://canu.readthedocs.io/en/latest/ <BR/> https://github.com/marbl/canu |
 | [Canu-Racon](https://hub.docker.com/r/staphb/canu-racon/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/canu-racon)](https://hub.docker.com/r/staphb/canu-racon) | <ul><li>1.7.1 (Canu), 1.3.1 (Racon), 2.13 (minimap2)</li><li>1.9 (Canu), 1.4.3 (Racon), 2.17 (minimap2)</li><li>1.9i (Canu), 1.4.3 (Racon), 2.17 (minimap2), (+racon_preprocess.py)</li><li>2.0 (Canu), 1.4.3 (Racon), 2.17 (minimap2)</li></ul> | https://canu.readthedocs.io/en/latest/ <br/> https://github.com/lbcb-sci/racon <br/> https://github.com/isovic/racon (ARCHIVED) <br/> https://lh3.github.io/minimap2/ |
-| [CAT](https://github.com/dutilh/CAT) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/cat)](https://hub.docker.com/r/staphb/cat) | <ul><li>[5.3](./cat/5.3)</li></ul> | https://github.com/dutilh/CAT |
+| [CAT](https://hub.docker.com/r/staphb/CAT) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/cat)](https://hub.docker.com/r/staphb/cat) | <ul><li>[5.3](./cat/5.3)</li><li>[6.0.1](./cat/6.0.1/)</li></ul> | https://github.com/dutilh/CAT / https://github.com/MGXlab/CAT_pack |
 | [centroid](https://hub.docker.com/r/staphb/centroid/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/centroid)](https://hub.docker.com/r/staphb/centroid) | <ul><li>1.0.0</li></ul> | https://github.com/stjacqrm/centroid |
 | [CDC-SPN](https://hub.docker.com/r/staphb/cdc-spn/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/cdc-spn)](https://hub.docker.com/r/staphb/cdc-spn) | <ul><li>0.1 (no version)</li></ul> | https://github.com/BenJamesMetcalf/Spn_Scripts_Reference |
 | [cfsan-snp-pipeline](https://hub.docker.com/r/staphb/cfsan-snp-pipeline) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/cfsan-snp-pipeline)](https://hub.docker.com/r/staphb/cfsan-snp-pipeline) | <ul><li>2.0.2</li> <li>2.2.1</li> </ul> | https://github.com/CFSAN-Biostatistics/snp-pipeline |

cat/6.0.1/Dockerfile

@@ -0,0 +1,126 @@
+# Set global variables
+ARG CAT_VER="6.0.1"
+ARG SAMTOOLS_VER="1.21"
+ARG BWA_VER="0.7.18"
+ARG DIAMOND_VER="2.1.10"
+
+
+FROM ubuntu:jammy AS builder
+
+ARG SAMTOOLS_VER
+ARG BWA_VER
+ARG DIAMOND_VER
+
+# install dependencies required for compiling samtools
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    libncurses5-dev \
+    libbz2-dev \
+    liblzma-dev \
+    libcurl4-gnutls-dev \
+    zlib1g-dev \
+    libssl-dev \
+    libdeflate-dev \
+    gcc \
+    wget \
+    make \
+    perl \
+    bzip2 \
+    gnuplot \
+    ca-certificates
+
+# download, compile, and install samtools
+RUN wget -q https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VER}/samtools-${SAMTOOLS_VER}.tar.bz2 && \
+    tar -xjf samtools-${SAMTOOLS_VER}.tar.bz2 && \
+    cd samtools-${SAMTOOLS_VER} && \
+    ./configure && \
+    make && \
+    make install
+
+
+RUN wget -q https://github.com/lh3/bwa/archive/refs/tags/v${BWA_VER}.tar.gz &&\
+    tar -xvf v${BWA_VER}.tar.gz &&\
+    cd bwa-${BWA_VER} &&\
+    make &&\
+    mv bwa /usr/local/bin/
+
+RUN wget -q https://github.com/bbuchfink/diamond/releases/download/v${DIAMOND_VER}/diamond-linux64.tar.gz &&\
+    tar -C /usr/local/bin -xvf diamond-linux64.tar.gz && \
+    rm diamond-linux64.tar.gz
+
+
+# Application Stage
+FROM ubuntu:jammy AS app
+ARG CAT_VER
+
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="CAT"
+LABEL software.version=${CAT_VER}
+LABEL description="CAT: a tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)."
+LABEL website="https://github.com/MGXlab/CAT_pack"
+LABEL license.url="https://github.com/MGXlab/CAT_pack/blob/master/LICENSE.md"
+LABEL maintainer="Taylor K. Paisie"
+LABEL maintainer.email='ltj8@cdc.gov'
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    unzip \
+    ca-certificates \
+    python3 \
+    python3-pip \
+    prodigal && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+COPY --from=builder /usr/local/bin/* /usr/local/bin/
+
+
+
+RUN wget -q https://github.com/MGXlab/CAT_pack/archive/refs/tags/v${CAT_VER}.tar.gz && \
+    tar -xvzf v${CAT_VER}.tar.gz && \
+    chmod +x /CAT_pack-${CAT_VER}/CAT_pack/CAT_pack && \
+    rm v${CAT_VER}.tar.gz
+
+
+# Add CAT to PATH
+ENV PATH="${PATH}:/CAT_pack-${CAT_VER}/CAT_pack"
+
+CMD ["CAT_pack", "--help"]
+WORKDIR /data
+
+# Optional stage: Test data
+FROM app AS test
+
+ARG CAT_VER
+
+WORKDIR /data/test
+
+RUN CAT_pack --help && CAT_pack --version
+
+RUN wget -nv --no-check-certificate \
+    https://raw.githubusercontent.com/taylorpaisie/docker_containers/main/checkm2/1.0.2/burk_wgs.fa \
+    -O burk_wgs_pos_ctrl.fa &&\
+    wget -nv --no-check-certificate \
+    https://merenlab.org/data/refining-mags/files/GN02_MAG_IV_B_1-contigs.fa \
+    -O GN02_MAG_IV_B_1-contigs.fa
+
+# Prepare testing database
+RUN mkdir -p db_tests && \
+    gzip -d /CAT_pack-${CAT_VER}/tests/data/prepare/small.fa.gz && \
+    CAT_pack prepare --db_fasta /CAT_pack-${CAT_VER}/tests/data/prepare/small.fa \
+    --acc2tax /CAT_pack-${CAT_VER}/tests/data/prepare/prot2acc.txt \
+    --names /CAT_pack-${CAT_VER}/tests/data/prepare/names.dmp \
+    --nodes /CAT_pack-${CAT_VER}/tests/data/prepare/nodes.dmp \
+    --db_dir db_tests/
+
+# Running CAT on contigs
+RUN CAT_pack contigs -c burk_wgs_pos_ctrl.fa \
+    -d db_tests/db \
+    -t db_tests/tax
+
+# Running BAT on a set of MAGs
+RUN CAT_pack bins -b GN02_MAG_IV_B_1-contigs.fa \
+    -d db_tests/db \
+    -t db_tests/tax
+
+WORKDIR /data

cat/6.0.1/README.md

@@ -0,0 +1,44 @@
+# CAT
+
+Main tool: [CAT](https://github.com/MGXlab/CAT_pack)
+
+Code repository: https://github.com/MGXlab/CAT_pack
+
+Basic information on how to use this tool:
+- executable: CAT_pack
+- help: --help
+- version: --version
+- description: | 
+> Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies
+
+
+Full documentation: https://github.com/MGXlab/CAT_pack
+
+
+# Testing CAT:
+```
+# Download test data
+wget -nv --no-check-certificate https://raw.githubusercontent.com/taylorpaisie/docker_containers/main/checkm2/1.0.2/burk_wgs.fa -O burk_wgs_pos_ctrl.fa
+
+wget -nv --no-check-certificate https://merenlab.org/data/refining-mags/files/GN02_MAG_IV_B_1-contigs.fa -O GN02_MAG_IV_B_1-contigs.fa
+
+# Prepare testing database
+RUN mkdir -p db_tests && \
+    gzip -d /CAT/tests/data/prepare/small.fa.gz && \
+    CAT_pack prepare --db_fasta /CAT/tests/data/prepare/small.fa \
+    --acc2tax /CAT/tests/data/prepare/prot2acc.txt \
+    --names /CAT/tests/data/prepare/names.dmp \
+    --nodes /CAT/tests/data/prepare/nodes.dmp \
+    --db_dir db_tests/
+
+# Use CAT and BAT for taxonomic classification for both best datasets
+# Running CAT on contigs
+CAT_pack contigs -c test/burk_wgs_pos_ctrl.fa \
+    -d db_tests/db \
+    -t db_tests/tax
+
+# Running BAT on a set of MAGs
+CAT_pack bins -b test/GN02_MAG_IV_B_1-contigs.fa \
+    -d db_tests/db \
+    -t db_tests/tax
+```