New Unicycler Dockerfile version 0.5.1

unicycler/0.5.1/Dockerfile

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+FROM ubuntu:focal as app
+
+# for easy upgrade later. ARG variables only persist during image build time
+ARG unicyclerVer="0.5.1"
+ARG blastVer="2.12.0"
+# the spades.py version is actually VERY important
+ARG spadesVer="3.15.4"
+ARG raconVer="1.4.3"
+
+LABEL base.image="ubuntu:focal"
+LABEL dockerfile.version="1"
+LABEL software="Unicycler"
+LABEL software.version="${unicyclerVer}"
+LABEL description="Unicycler is an assembly pipeline for bacterial genomes."
+LABEL website="https://github.com/rrwick/Unicycler"
+LABEL license="https://github.com/rrwick/Unicycler/blob/main/LICENSE"
+LABEL maintainer1="Kelsey Florek"
+LABEL maintainer1.email="kelsey.florek@slh.wisc.edu"
+LABEL maintainer2="Curtis Kapsak"
+LABEL maintainer2.email="kapsakcj@gmail.com"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="eriny@utah.gov"
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+# install dependencies; cleanup apt garbage
+RUN apt-get update && apt-get install --no-install-recommends -y \
+  python3 \
+  python3-pip \
+  python3-distutils \
+  python-setuptools \
+  cmake \
+  build-essential \
+  wget \
+  libgomp1 \
+  libz-dev \
+  ca-certificates && \
+  apt-get autoclean && rm -rf /var/lib/apt/lists/* && \
+  # python v3.8.10 is installed here; point 'python' to python3
+  update-alternatives --install /usr/bin/python python /usr/bin/python3 10
+
+# install SPAdes binary
+RUN wget https://github.com/ablab/spades/releases/download/v${spadesVer}/SPAdes-${spadesVer}-Linux.tar.gz && \
+  tar -xzf SPAdes-${spadesVer}-Linux.tar.gz && \
+  rm -v SPAdes-${spadesVer}-Linux.tar.gz
+
+# ncbi-blast+
+# ubuntu:focal apt version of blast is old-ish (2.9.0)
+RUN wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${blastVer}/ncbi-blast-${blastVer}+-x64-linux.tar.gz && \
+  tar -xzf ncbi-blast-${blastVer}+-x64-linux.tar.gz && \
+  rm ncbi-blast-${blastVer}+-x64-linux.tar.gz
+
+# get racon
+RUN wget https://github.com/isovic/racon/releases/download/${raconVer}/racon-v${raconVer}.tar.gz && \
+  mkdir racon && \
+  tar -xzvf racon-v${raconVer}.tar.gz -C racon --strip-components 1 && \
+  rm racon-v${raconVer}.tar.gz && \
+  cd racon && \
+  mkdir build && \
+  cd build && \
+# for installing racon tests
+  cmake -DCMAKE_BUILD_TYPE=Release -Dracon_build_tests=ON ../ && \
+  cmake -DCMAKE_BUILD_TYPE=Release ../ && \
+  make && \
+  make install
+
+# LC_ALL for singularity compatibility
+# set PATH so that blast binaries and spades.py are available during unicycler install
+# TERM set so that output is pretty during tests - also ensures unicycler unit tests pass 
+ENV PATH="/SPAdes-${spadesVer}-Linux/bin:/ncbi-blast-${blastVer}+/bin/:${PATH}" \
+ LC_ALL=C.UTF-8 \
+ TERM=xterm-256color
+
+# get unicycler; install
+RUN wget https://github.com/rrwick/Unicycler/archive/v${unicyclerVer}.tar.gz && \
+  mkdir unicycler && \
+  tar -xzvf v${unicyclerVer}.tar.gz -C unicycler --strip-components 1 && \
+  rm v${unicyclerVer}.tar.gz && \
+  python3 /unicycler/setup.py install && \
+  mkdir /data
+
+# final working directory in app layer is /data, as usual
+WORKDIR /data
+
+FROM app as test
+
+# test spades and unicycler unit tests
+RUN spades.py --test && \
+  cd /unicycler && python -m unittest
+
+# test racon; added in to make sure that racon wasn't an issue
+RUN /racon/build/bin/racon_test 
+
+# testing on the test data (ILMN and ONT) provided with unicycler code
+RUN unicycler --version && unicycler --help && \
+  unicycler -1 /unicycler/sample_data/short_reads_1.fastq.gz \
+  -2 /unicycler/sample_data/short_reads_2.fastq.gz \
+  -l /unicycler/sample_data/long_reads_high_depth.fastq.gz \
+  --out sample_data_hybrid_asm_test

unicycler/0.5.1/README.md

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+# Unicycler container
+
+Main tools:
+- [Unicycler](https://github.com/rrwick/Unicycler)
+
+Other tools:
+- [spades](https://github.com/ablab/spades)
+- [racon](https://github.com/isovic/racon)
+
+Unicycler is a hybrid assembler that takes reads assembled with spades and ties them together with long reads.
+
+# Example Usage
+
+```
+unicycler -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -l long_reads.fastq.gz -o output_dir
+```
+
+Better documentation can be found at [https://github.com/rrwick/Unicycler](https://github.com/rrwick/Unicycler)