Update Minipolish to 0.2.1

README.md

@@ -233,7 +233,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [metaphlan](https://hub.docker.com/r/staphb/metaphlan) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/metaphlan)](https://hub.docker.com/r/staphb/metaphlan) | <details><summary>Click to see all versions</summary> <ul><li>[3.0.3-no-db (no database)](./build-files/metaphlan/3.0.3-no-db/)</li><li>[3.0.3 (~3GB db)](./build-files/metaphlan/3.0.3/)</li><li>[4.1.0](./build-files/metaphlan/4.1.0/) (no database)</li><li>[4.1.1](./build-files/metaphlan/4.1.1/) (no database)</li><li>[4.2.2](./build-files/metaphlan/4.2.2/)</li><li>[4.2.4](./build-files/metaphlan/4.2.4/)</li></ul> </details> | https://github.com/biobakery/MetaPhlAn |
 | [MIDAS](https://hub.docker.com/r/staphb/midas) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/midas)](https://hub.docker.com/r/staphb/midas) | <details><summary>Click to see all versions</summary> <ul><li>[1.3.2 (no database)](./build-files/midas/1.3.2/)</li>| https://github.com/snayfach/MIDAS |
 | [minimap2](https://hub.docker.com/r/staphb/minimap2) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/minimap2)](https://hub.docker.com/r/staphb/minimap2) | <details><summary>Click to see all versions</summary> <ul><li>[2.17](./build-files/minimap2/2.17/)</li><li>[2.18](./build-files/minimap2/2.18/)</li><li>[2.21](./build-files/minimap2/2.21/)</li><li>[2.22](./build-files/minimap2/2.22/)</li><li>[2.23](./build-files/minimap2/2.23/)</li><li>[2.24](./build-files/minimap2/2.24/)</li><li>[2.25](./build-files/minimap2/2.25/)</li><li>[2.26](./build-files/minimap2/2.26)</li><li>[2.27](./build-files/minimap2/2.27/)</li><li>[2.28](./build-files/minimap2/2.28/)</li><li>[2.29](./build-files/minimap2/2.29/)</li><li>[2.30](./build-files/minimap2/2.30/)</li></ul></details> | https://github.com/lh3/minimap2 |
-| [minipolish](https://hub.docker.com/r/staphb/minipolish) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/minipolish)](https://hub.docker.com/r/staphb/minipolish) | <details><summary>Click to see all versions</summary> <ul><li>[0.1.3](./build-files/minipolish/0.1.3/)</li><li>[0.2.0](./build-files/minipolish/0.2.0/)</li></ul> </details> | https://github.com/rrwick/Minipolish |
+| [minipolish](https://hub.docker.com/r/staphb/minipolish) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/minipolish)](https://hub.docker.com/r/staphb/minipolish) | <details><summary>Click to see all versions</summary> <ul><li>[0.1.3](./build-files/minipolish/0.1.3/)</li><li>[0.2.0](./build-files/minipolish/0.2.0/)</li><li>[0.2.1](./build-files/minipolish/0.2.1/)</li></ul> </details> | https://github.com/rrwick/Minipolish |
 | [mlst](https://hub.docker.com/r/staphb/mlst) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mlst)](https://hub.docker.com/r/staphb/mlst) | <details><summary>Click to see all versions</summary> <ul><li>[2.16.2](./build-files/mlst/2.16.2/)</li><li>[2.17.6](./build-files/mlst/2.17.6/)</li><li>[2.19.0](./build-files/mlst/2.19.0/)</li><li>[2.22.0](./build-files/mlst/2.22.0/)</li><li>[2.22.1](./build-files/mlst/2.22.1/)</li><li>[2.23.0](./build-files/mlst/2.23.0/)</li><li>[2.23.0-2023-07](./build-files/mlst/2.23.0-2023-07/)</li><li>[2.23.0-2023-08](./build-files/mlst/2.23.0-2023-08/)</li><li>[2.23.0-2024-01](./build-files/mlst/2.23.0-2024-01/)</li><li>[2.23.0-2024-03](./build-files/mlst/2.23.0-2024-12/)</li><li>[2.23.0-2024-12-31](./build-files/mlst/2.23.0-2024-12-31/)</li><li>[2.25.0](./build-files/mlst/2.25.0/)</li><li>[2.28.1](./build-files/mlst/2.28.1/)</li><li>[2.32.2](./build-files/mlst/2.32.2/)</li></ul> </details> | https://github.com/tseemann/mlst |
 | [MMseqs2](https://hub.docker.com/r/staphb/mmseqs2) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mmseqs2)](https://hub.docker.com/r/staphb/mmseqs2) | <details><summary>Click to see all versions</summary> <ul><li>[17-b804f](./build-files/mmseqs2/17-b804f/)</li><li>[18-8cc5c](./build-files/mmseqs2/18-8cc5c/)</li></ul> </details> | https://github.com/soedinglab/MMseqs2 |
 | [mob-suite](https://github.com/phac-nml/mob-suite) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mob-suite)](https://hub.docker.com/r/staphb/mob-suite) | <details><summary>Click to see all versions</summary> <ul><li>[3.1.9](./build-files/mob-suite/3.1.9/)</li></ul> </details> | https://github.com/phac-nml/mob-suite |

build-files/minipolish/0.2.1/Dockerfile

@@ -0,0 +1,116 @@
+ARG MINIPOLISH_VER=0.2.1
+ARG MINIMAP2_VER=2.30
+ARG RACON_VER=1.5.0
+ARG MINIASM_VER=0.3
+
+FROM ubuntu:noble AS builder
+ARG MINIPOLISH_VER
+ARG MINIMAP2_VER
+ARG RACON_VER
+ARG MINIASM_VER
+
+# Install dependencies
+RUN apt-get update && apt-get install --no-install-recommends -y \
+  perl \
+  default-jre \
+  gnuplot \
+  libgomp1 \
+  maven \
+  git \
+  wget \
+  python3 \
+  build-essential \
+  cmake \
+  zlib1g-dev \
+  curl \
+  bzip2 && \
+  apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# Install Racon
+RUN wget https://github.com/lbcb-sci/racon/archive/refs/tags/${RACON_VER}.tar.gz && \
+  tar -xvf ${RACON_VER}.tar.gz && \
+  cd racon-${RACON_VER} && \
+  mkdir build && \
+  cd build && \
+  cmake -DCMAKE_BUILD_TYPE=Release .. && \
+  make
+
+# Add Racon to PATH
+ENV PATH="/racon-${RACON_VER}/build/bin:${PATH}"
+
+# Test Racon
+RUN racon_test
+
+# Install Minimap2
+RUN curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VER}/minimap2-${MINIMAP2_VER}_x64-linux.tar.bz2 | tar -jxvf - --no-same-owner && \
+    mv minimap2-${MINIMAP2_VER}_x64-linux /usr/local/bin/minimap2
+
+# miniasm
+RUN wget https://github.com/lh3/miniasm/archive/v${MINIASM_VER}.tar.gz && \
+  mkdir miniasm && \
+  tar -xzvf v${MINIASM_VER}.tar.gz -C miniasm --strip-components 1 && \
+  rm v${MINIASM_VER}.tar.gz && \
+  cd miniasm && \
+  make && \
+  mv miniasm /usr/local/bin/.
+
+FROM ubuntu:noble AS app
+ARG MINIPOLISH_VER
+ARG RACON_VER
+
+# metadata
+LABEL base.image="ubuntu:noble"
+LABEL dockerfile.version="1"
+LABEL software="minipolish"
+LABEL software.version="${MINIPOLISH_VER}"
+LABEL description="Racon polishing for GFA graphs produced by miniasm"
+LABEL website="https://github.com/rrwick/Minipolish"
+LABEL license="https://github.com/rrwick/Minipolish/blob/main/LICENSE"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="eriny@utah.gov"
+
+# install dependencies via apt-get or yum if using a centos or fedora base
+RUN apt-get update && apt-get install -y --no-install-recommends \
+  wget \
+  ca-certificates \
+  python3-pip && \
+  apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+COPY --from=builder /racon-${RACON_VER}/build/bin/* /usr/local/bin/
+COPY --from=builder /usr/local/bin/* /usr/local/bin/
+
+# install minipolish
+RUN wget https://github.com/rrwick/Minipolish/archive/refs/tags/v${MINIPOLISH_VER}.tar.gz && \
+  tar -vxf v${MINIPOLISH_VER}.tar.gz && \
+  pip install --break-system-packages v${MINIPOLISH_VER}.tar.gz && \
+  rm v${MINIPOLISH_VER}.tar.gz 
+# in theory, this can be tested with python3 -m pytest
+
+# set environmental variables e.g. $PATH and locale settings for singularity compatibility
+ENV PATH="/Minipolish-${MINIPOLISH_VER}:${PATH}" \
+  TERM=xterm-256color \
+  LC_ALL=C
+
+# set working directory
+WORKDIR /data
+
+CMD ["minipolish", "--help"]
+
+FROM app AS test
+
+RUN minipolish --help
+
+# checking dependencies
+RUN minimap2 --version && racon --help && miniasm -V
+
+WORKDIR /test
+
+RUN wget https://github.com/rrwick/Unicycler/raw/refs/heads/main/sample_data/long_reads_high_depth.fastq.gz
+
+#RUN miniasm_and_minipolish.sh long_reads_high_depth.fastq.gz 4 > test.gfa && head test.gfa
+
+# Testing the test data without using the wrapper script
+RUN minimap2 -x ava-ont -t 4 long_reads_high_depth.fastq.gz long_reads_high_depth.fastq.gz > overlaps.paf && \
+    miniasm -f long_reads_high_depth.fastq.gz overlaps.paf -s 50 -e 1 > test.gfa && \
+    minipolish --threads 4 long_reads_high_depth.fastq.gz test.gfa > polished.gfa && \
+    head polished.gfa

build-files/minipolish/0.2.1/README.md

@@ -0,0 +1,22 @@
+# minipolish and miniasm container
+
+Main tool : [minipolish](https://github.com/rrwick/Minipolish) and [miniasm](https://github.com/lh3/miniasm)
+
+Other tools :
+- [racon](https://github.com/isovic/racon)  version 1.5.0
+- [minimap2](https://github.com/lh3/minimap2) version 2.30
+- [miniasm](https://github.com/lh3/miniasm) version 0.3
+
+From minipolish's [readme](https://github.com/rrwick/Minipolish):
+
+> Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not include a polishing step, so its assemblies have a high error rate – they are essentially made of stitched-together pieces of long reads.
+>
+> Racon is a great polishing tool that can be used to clean up assembly errors. It's also very fast and well suited for long-read data. However, it operates on FASTA files, not the GFA graphs that miniasm makes.
+>
+> That's where Minipolish comes in. With a single command, it will use Racon to polish up a miniasm assembly, while keeping the assembly in graph form.
+
+# Example Usage
+
+```
+miniasm_and_minipolish.sh input.fastq $threads > output.gfa
+```