added example usage (#877)

Program_Licenses.md

@@ -122,6 +122,7 @@ The licenses of the open-source software that is contained in these Docker image
 | Prokka | GNU GPLv3 | https://raw.githubusercontent.com/tseemann/prokka/master/doc/LICENSE.Prokka |
 | pyCirclize | MIT | https://github.com/moshi4/pyCirclize/blob/main/LICENSE |
 | pyGenomeViz | MIT | https://github.com/moshi4/pyGenomeViz/blob/main/LICENSE |
+| pypolca | MIT | https://github.com/gbouras13/pypolca/blob/main/LICENSE |
 | QUAST | GNU GPLv2 | https://github.com/ablab/quast/blob/master/LICENSE.txt |
 | QuickSNP | GNU GPLv3 | https://github.com/k-florek/QuickSNP/blob/main/LICENSE |
 | racon | MIT | https://github.com/lbcb-sci/racon/blob/master/LICENSE ; https://github.com/isovic/racon/blob/master/LICENSE |

README.md

@@ -227,6 +227,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [Prokka](https://hub.docker.com/r/staphb/prokka/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/prokka)](https://hub.docker.com/r/staphb/prokka) | <ul><li>1.13.4</li><li>1.14.0</li><li>1.14.5</li><li>1.14.6</li></ul> | https://github.com/tseemann/prokka |
 | [pyCirclize](https://hub.docker.com/r/staphb/pycirclize/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pycirclize)](https://hub.docker.com/r/staphb/pycirclize) | <ul><li>[1.0.0](pycirclize/1.0.0/)</li><li>[1.2.0](./pycirclize/1.2.0/)</li></ul> | https://github.com/moshi4/pyCirclize |
 | [pyGenomeViz](https://hub.docker.com/r/staphb/pygenomeviz/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pygenomeviz)](https://hub.docker.com/r/staphb/pygenomeviz) | <ul><li>0.2.2</li><li>0.3.2</li><li>[0.4.2](pygenomeviz/0.4.2/)</li><li>[0.4.3](pygenomeviz/0.4.3/)</li><li>[0.4.4](pygenomeviz/0.4.4/)</li></ul> | https://github.com/moshi4/pyGenomeViz |
+| [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></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> |

pypolca/0.3.1/Dockerfile

@@ -0,0 +1,62 @@
+# both of these use the ubuntu:jammy base
+FROM staphb/freebayes:1.3.7 as freebayes
+FROM staphb/samtools:1.19 as samtools
+
+FROM ubuntu:jammy as app
+
+ARG PYPOLCA_VER="0.3.1"
+
+# 'LABEL' instructions tag the image with metadata that might be important to the user
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="pypolca"
+LABEL software.version="${PYPOLCA_VER}"
+LABEL description="Polishes long reads"
+LABEL website="https://github.com/gbouras13/pypolca"
+LABEL license="https://github.com/gbouras13/pypolca/blob/main/LICENSE"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="[email protected]"
+
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    procps \
+    ca-certificates \
+    wget \
+    bwa \
+    vcftools \
+    libseqlib-dev \
+    libvcflib-tools \
+    parallel \
+    bc \
+    python3 \
+    python3-pip && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+COPY --from=freebayes /usr/local/bin/* /usr/local/bin/
+COPY --from=samtools  /usr/local/bin/* /usr/local/bin/
+
+RUN pip3 install --no-cache pypolca==${PYPOLCA_VER}
+
+ENV PATH="$PATH" \
+    LC_ALL=C
+
+# 'CMD' instructions set a default command when the container is run. This is typically 'tool --help.'
+CMD pypolca -h
+
+# 'WORKDIR' sets working directory
+WORKDIR /data
+
+# A second FROM insruction creates a new stage
+FROM app as test
+
+WORKDIR /test
+
+RUN pypolca -h && \
+    pypolca --version
+
+RUN wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123_1.fastq.gz && \
+    wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123_2.fastq.gz && \
+    wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.consensus.fa && \
+    pypolca run -a SRR13957123.consensus.fa -1 SRR13957123_1.fastq.gz -2 SRR13957123_2.fastq.gz  -t 2 -o test && \
+    head test/pypolca_*.log && \
+    ls test/pypolca.report test/pypolca.vcf test/pypolca_corrected.fasta

pypolca/0.3.1/README.md

@@ -0,0 +1,27 @@
+# pypolca container
+
+Main tool: [pypolca](https://github.com/gbouras13/pypolca)
+
+Code repository:
+
+Additional tools:
+- samtools: 1.19
+- vcftools: 0.1.16
+- bwa: 0.7.17-r1188
+- freebayes: 1.3.7
+
+Basic information on how to use this tool:
+- executable: pypolca
+- help: pypolca -h
+- version: pypolca -v
+- description: Polished long-read assemblies with Illumina reads
+
+> pypolca is a Standalone Python re-implementation of the POLCA polisher from the MaSuRCA genome assembly and analysis toolkit.
+  
+Full documentation: [https://github.com/rrwick/Polypolish](https://github.com/rrwick/Polypolish)
+
+## Example Usage
+
+```bash
+pypolca run -a assembly.fasta -1 R1.fastq.gz -2 R2.fastq.gz -t 4 -o output 
+```