adding canu version 2.3

README.md

@@ -134,7 +134,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [Bracken](https://hub.docker.com/r/staphb/bracken/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bracken)](https://hub.docker.com/r/staphb/bracken) | <ul><li>[2.9](./bracken/2.9)</li></ul> | https://ccb.jhu.edu/software/bracken/index.shtml?t=manual <br/>https://github.com/jenniferlu717/Bracken |
 | [BUSCO](https://hub.docker.com/r/staphb/busco/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/busco)](https://hub.docker.com/r/staphb/busco) | <ul><li>[5.4.7](./busco/5.4.7/)</li><li>[5.6.1](./busco/5.6.1/)</li><li>[5.6.1-prok-bacteria_odb10_2024-01-08](./busco/5.6.1-prok-bacteria_odb10_2024-01-08/)</li><li>[5.7.1](./busco/5.7.1/)</li><li>[5.7.1-prok-bacteria_odb10_2024-01-08](./busco/5.7.1-prok-bacteria_odb10_2024-01-08/)</li><li>[5.8.0](./busco/5.8.0/)</li><li>[5.8.0-prok-bacteria_odb10_2024-01-08](./busco/5.8.0-prok-bacteria_odb10_2024-01-08/)</li><li>[5.8.2](./busco/5.8.2/)</li><li>[5.8.2-prok-bacteria_odb10_2024-11-14](./busco/5.8.2-prok-bacteria_odb10_2024-11-14/)</li></ul> | https://busco.ezlab.org/busco_userguide.html <br/>https://gitlab.com/ezlab/busco |
 | [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](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](./build-files/canu/2.0/)</li><li>[2.1.1](./build-files/canu/2.1.1/)</li><li>[2.2](./build-files/canu/2.2/)</li><li>[2.3](./build-files/canu/2.3/)</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 |
 | [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 |

build-files/canu/2.3/Dockerfile

@@ -0,0 +1,77 @@
+# Use ubuntu as base image
+FROM ubuntu:jammy AS app
+
+ARG CANU_VERSION="2.3"
+
+# metadata
+LABEL base.image="ubuntu:jammy"
+LABEL software="Canu"
+LABEL software.version="${CANU_VERSION}"
+LABEL dockerfile.version="1"
+LABEL description="Long read assembly and polishing tools"
+LABEL website="https://github.com/marbl/canu"
+LABEL license="https://github.com/marbl/canu/blob/master/README.license.GPL"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="[email protected]"
+
+# dependencies
+# samtools version 1.13
+# gnuplot version 5.4 patchlevel 2
+RUN apt-get update && apt-get install -y --no-install-recommends \
+   perl \
+   samtools \
+   default-jre \
+   gnuplot \
+#   libgcc-5-dev \
+   libgomp1 \
+#   maven \
+#   git \
+   wget \
+   ca-certificates \
+   xz-utils \
+   minimap2 \
+#   python3 \
+#   build-essential \
+#   cmake \
+#   zlib1g-dev 
+   && \
+   apt-get autoclean && rm -rf /var/lib/apt/lists/* && \
+   mkdir /data
+
+# install canu
+RUN wget https://github.com/marbl/canu/releases/download/v${CANU_VERSION}/canu-${CANU_VERSION}.Linux-amd64.tar.xz && \
+   tar -xvf canu-${CANU_VERSION}.Linux-amd64.tar.xz && \
+   rm canu-${CANU_VERSION}.Linux-amd64.tar.xz
+
+ENV PATH="/canu-${CANU_VERSION}/bin:${PATH}"
+
+CMD ["canu", "-h"]
+
+WORKDIR /data
+
+# set perl locale settings
+ENV LC_ALL=C
+
+# ======== Adding a test layer ========
+
+FROM app AS test
+
+RUN canu -h
+
+# creating test working DIR.  
+WORKDIR /test_canu
+
+# download test input file into /test_canu/ directory
+RUN wget -q https://raw.githubusercontent.com/bactopia/bactopia-tests/main/data/species/portiera/nanopore/ERR3772599.fastq.gz
+
+# testing analysis RUN, canu need to know approx genome size (for coverage calculation) and sequencing platform
+RUN canu \
+   -p portiera -d portiera-nanopore \
+   genomeSize=0.3m \
+   -nanopore ERR3772599.fastq.gz \
+   maxMemory=7 maxThreads=2 \
+   redMemory=7 redThreads=2 \
+   corMemory=7 corThreads=2 \
+   oeaMemory=7 oeaThreads=2 \
+   batMemory=7 batThreads=2 \
+   cnsMemory=7 cnsThreads=2 

build-files/canu/2.3/README.md

@@ -0,0 +1,11 @@
+# Canu container
+
+Main tool : [Canu](https://github.com/marbl/canu)
+
+Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
+
+## Example Usage
+
+```bash
+canu -p {sample} genomeSize={genome.length} -nanopore {input.fastq}
+```