Update Racon 1.5.0 to include minimap2

README.md

@@ -257,7 +257,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [pypolca](https://hub.docker.com/r/staphb/pypolca/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pypolca)](https://hub.docker.com/r/staphb/pypolca) | <ul><li>[0.3.1](./pypolca/0.3.1/)</li></ul> | https://github.com/gbouras13/pypolca |
 | [QUAST](https://hub.docker.com/r/staphb/quast/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/quast)](https://hub.docker.com/r/staphb/quast) | <ul><li>5.0.0</li><li>5.0.2</li><li>[5.2.0](./quast/5.2.0)</li><li>[5.2.0-slim](./quast/5.2.0-slim)</li><li>[5.3.0](./quast/5.3.0)</li><li>[5.3.0-slim](./quast/5.3.0-slim)</li></ul> | https://github.com/ablab/quast |
 | [QuickSNP](https://hub.docker.com/r/staphb/quicksnp/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/quicksnp)](https://hub.docker.com/r/staphb/quicksnp) | <ul><li>1.0.1</li></ul> | https://github.com/k-florek/QuickSNP |
-| [racon](https://hub.docker.com/r/staphb/racon) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/racon)](https://hub.docker.com/r/staphb/racon)| <ul><li>[1.4.3](./racon/1.4.3/)</li><li>[1.4.20](./racon/1.4.20/)</li><li>[1.5.0](./racon/1.5.0/)</li></ul> | <li> https://github.com/lbcb-sci/racon </li><li> https://github.com/isovic/racon (ARCHIVED)</li> |
+| [racon](https://hub.docker.com/r/staphb/racon) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/racon)](https://hub.docker.com/r/staphb/racon)| <ul><li>[1.4.3](./racon/1.4.3/)</li><li>[1.4.20](./racon/1.4.20/)</li><li>[1.5.0](./racon/1.5.0/)</li><li>[1.5.0-minimap2](./racon/1.5.0-minimap2/)</li></ul> | <li> https://github.com/lbcb-sci/racon </li><li> https://github.com/isovic/racon (ARCHIVED)</li> |
 | [rasusa](https://hub.docker.com/r/staphb/rasusa/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/rasusa)](https://hub.docker.com/r/staphb/rasusa) | <ul><li>[0.1.0](./rasusa/0.1.0/)</li><li>[0.2.0](./rasusa/0.2.0/)</li><li>[0.3.0](./rasusa/0.3.0/)</li><li>[0.6.0](./rasusa/0.6.0/)</li><li>[0.7.0](./rasusa/0.7.0/)</li><li>[0.8.0](./rasusa/0.8.0/)</li><li>[2.0.0](./rasusa/2.0.0/)</li><li>[2.1.0](./rasusa/2.1.0/)</li></ul> | https://github.com/mbhall88/rasusa |
 | [raven](https://hub.docker.com/r/staphb/raven/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/raven)](https://hub.docker.com/r/staphb/raven) | <ul><li>1.5.1</li><li>1.8.1</li><li>[1.8.3](./raven/1.8.3)</li></ul> | https://github.com/lbcb-sci/raven |
 | [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 |

racon/1.5.0-minimap2/Dockerfile

@@ -0,0 +1,104 @@
+ARG RACON_VER="1.5.0"
+ARG MINIMAP2_VER="2.28"
+
+# Use ubuntu as base image
+FROM ubuntu:jammy AS builder
+
+ARG RACON_VER
+ARG MINIMAP2_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-${MINIMAP2_VER}_x64-linux /usr/local/minimap2
+
+# Add Minimap2 to PATH
+ENV PATH="/usr/local/minimap2:${PATH}"
+
+# Test Minimap2
+RUN minimap2 --version
+
+FROM ubuntu:jammy AS app
+
+ARG RACON_VER
+ARG MINIMAP2_VER
+
+# Metadata
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="Racon + Minimap2"
+LABEL racon.version="${RACON_VER}"
+LABEL minimap2.version="${MINIMAP2_VER}"
+LABEL description="Racon for assembly polishing and Minimap2 for alignment"
+LABEL website="https://github.com/lbcb-sci/racon, https://github.com/lh3/minimap2"
+LABEL license="https://github.com/lbcb-sci/racon/blob/master/LICENSE, https://github.com/lh3/minimap2/blob/master/LICENSE.txt"
+LABEL maintainer="Fraser Combe"
+LABEL maintainer.email="[email protected]"
+
+# Install Python and essential tools
+RUN apt-get update && apt-get install -y \
+  procps \
+  wget \
+  python3 && \
+  apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# Copy Racon and Minimap2 binaries
+COPY --from=builder /racon-${RACON_VER}/build/bin/* /usr/local/bin/
+COPY --from=builder /usr/local/minimap2/* /usr/local/bin/
+
+RUN mkdir /data
+
+WORKDIR /data
+
+# Set locale settings
+ENV PATH=${PATH} LC_ALL=C
+
+CMD racon --help
+
+FROM app AS test
+
+# Test Racon and Minimap2
+RUN racon --help && racon --version && minimap2 --version
+
+COPY --from=builder /racon-${RACON_VER}/test/data/* /test/
+
+WORKDIR /test
+
+# Example polishing workflow
+RUN wget -q https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf && \
+  wget -q https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz && \
+  wget -q https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz && \
+  minimap2 -x map-ont genome.fna.gz test.fastq.gz > test.paf && \
+  racon -t 2 test.fastq.gz test.paf genome.fna.gz > test_polished.fasta && \
+  head test_polished.fasta

racon/1.5.0/README.md

@@ -1,23 +1,46 @@
-# racon container
+# Racon + Minimap2 Container
 
-Main tool : [racon](https://github.com/lbcb-sci/racon)
+This container combines [Racon](https://github.com/lbcb-sci/racon) and [Minimap2](https://github.com/lh3/minimap2) for efficient polishing and alignment in long-read assembly workflows.
 
-Code repository: https://github.com/lbcb-sci/racon
+## Tools Included
+- **Racon**: Polishes long-read assemblies.
+- **Minimap2**: Generates alignments for use with Racon and other polishing tools.
 
-Basic information on how to use this tool:
-- executable: racon
-- help: -h
-- version: -v
-- description: Polishes long read assemblies
+### Code Repositories
+- Racon: [GitHub Repository](https://github.com/lbcb-sci/racon)
+- Minimap2: [GitHub Repository](https://github.com/lh3/minimap2)
 
-> Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step.
+## Basic Information
 
-# Example Usage
+### Racon
+- **Executable**: `racon`
+- **Help**: `racon -h`
+- **Version**: `racon -v`
+- **Description**: 
+  > Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods that do not include a consensus step.
+
+### Minimap2
+- **Executable**: `minimap2`
+- **Help**: `minimap2 -h`
+- **Version**: `minimap2 --version`
+- **Description**: 
+  > Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.
+
+## Example Usage
 
 ```bash
-# general
+# Racon general
 racon <sequences> <overlaps> <target sequences>
 
 # more specific
 racon --match 8 --mismatch -6 --gap -8 --window-length 500 --threads {threads} {input.reads} {input.alignment} {input.assembly}
+
+#Combined Racon and Minimap2 Workflow
+
+#Align Reads to Assembly Using Minimap2:
+minimap2 -x map-ont <assembly.fasta> <reads.fastq> > overlaps.paf
+
+#polish assembly using Racon
+racon --threads {threads} <reads.fastq> overlaps.paf <assembly.fasta> > polished_assembly.fasta
 ```
+