add bwa to polypolish 0.6.0

README.md

@@ -246,7 +246,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [PlasmidSeeker](https://hub.docker.com/r/staphb/plasmidseeker) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/plasmidseeker)](https://hub.docker.com/r/staphb/plasmidseeker) | <ul><li>1.0</li><li>1.3</li></ul> | https://github.com/bioinfo-ut/PlasmidSeeker |
 | [pmga](https://hub.docker.com/r/staphb/pmga/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pmga)](https://hub.docker.com/r/staphb/pmga) | <ul><li>3.0.2</li></ul> | https://github.com/rpetit3/pmga |
 | [PolkaPox](https://hub.docker.com/r/staphb/polkapox/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/polkapox)](https://hub.docker.com/r/staphb/polkapox) | <ul><li>[1.0.0-beta](./polkapox/1.0.0-beta/)</li></ul> | https://github.com/CDCgov/polkapox |
-| [polypolish](https://hub.docker.com/r/staphb/polypolish/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/polypolish)](https://hub.docker.com/r/staphb/polypolish) | <ul><li>[0.5.0](./polypolish/0.5.0/)</li><li>[0.6.0](./polypolish/0.6.0/)</li></ul> | https://github.com/rrwick/Polypolish |
+| [polypolish](https://hub.docker.com/r/staphb/polypolish/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/polypolish)](https://hub.docker.com/r/staphb/polypolish) | <ul><li>[0.5.0](./polypolish/0.5.0/)</li><li>[0.6.0](./polypolish/0.6.0/)</li><li>[0.6.0-bwa](./polypolish/0.6.0-bwa/)</li></ul> | https://github.com/rrwick/Polypolish |
 | [PopPUNK](https://hub.docker.com/r/staphb/poppunk/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/poppunk)](https://hub.docker.com/r/staphb/poppunk) | <ul><li>[2.4.0](./poppunk/2.4.0/)</li><li>[2.5.0](./poppunk/2.5.0/)</li><li>[2.6.0](./poppunk/2.6.0/)</li><li>[2.6.2](./poppunk/2.6.2/)</li><li>[2.6.3](./poppunk/2.6.3/)</li><li>[2.6.5](./poppunk/2.6.5/)</li></ul> | https://github.com/bacpop/PopPUNK |
 | [Porechop](https://hub.docker.com/r/staphb/porechop/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/porechop)](https://hub.docker.com/r/staphb/porechop) | <ul><li>0.2.4</li></ul> | https://github.com/rrwick/Porechop |
 | [PPanGGOLiN](https://hub.docker.com/r/staphb/ppanggolin/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ppanggolin)](https://hub.docker.com/r/staphb/ppanggolin) | <ul><li>[1.2.105](./ppanggolin/1.2.105/)</li><li>[2.0.3](./ppanggolin/2.0.3/)</li><li>[2.0.5](./ppanggolin/2.0.5/)</li><li>[2.1.2](./ppanggolin/2.1.2/)</li></ul> | https://github.com/labgem/PPanGGOLiN |

polypolish/0.6.0-bwa/Dockerfile

@@ -0,0 +1,70 @@
+ARG POLYPOLISH_VER="0.6.0"
+ARG BWA_VER="0.7.18"
+
+FROM rust:1.75 AS builder
+
+ARG POLYPOLISH_VER
+ARG BWA_VER
+
+RUN wget -q https://github.com/rrwick/Polypolish/archive/refs/tags/v${POLYPOLISH_VER}.tar.gz && \
+    tar -vxf v${POLYPOLISH_VER}.tar.gz && \
+    cd /Polypolish-${POLYPOLISH_VER} && \
+    cargo build --release 
+
+RUN wget https://github.com/lh3/bwa/archive/refs/tags/v${BWA_VER}.tar.gz &&\
+    tar -xvf v${BWA_VER}.tar.gz &&\
+    cd bwa-${BWA_VER} &&\
+    make &&\
+    mv bwa /usr/local/bin/
+
+FROM ubuntu:jammy AS app
+
+ARG POLYPOLISH_VER
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="polypolish"
+LABEL software.version="${POLYPOLISH_VER}"
+LABEL description="Polypolish is a tool for polishing genome assemblies with short reads."
+LABEL website="https://github.com/rrwick/Polypolish"
+LABEL license="https://github.com/rrwick/Polypolish/blob/main/LICENSE"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="[email protected]"
+LABEL maintainer2="Sage Wright"
+LABEL maintainer2.email="[email protected]"
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    procps \
+    unzip \
+    python3 && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+COPY --from=builder /Polypolish-${POLYPOLISH_VER}/target/release/polypolish /usr/local/bin/polypolish
+COPY --from=builder /usr/local/bin/bwa /usr/local/bin/
+
+ENV LC_ALL=C
+
+CMD ["polypolish", "--help"]
+
+WORKDIR /data
+
+FROM app AS test
+
+RUN polypolish --help && polypolish --version
+
+# using "toy" data
+RUN wget -q https://raw.githubusercontent.com/wiki/rrwick/Polypolish/files/toy_example/assembly.fasta && \
+    wget -q https://raw.githubusercontent.com/wiki/rrwick/Polypolish/files/toy_example/alignments.sam && \
+    polypolish polish assembly.fasta alignments.sam > polished.fasta
+
+# testing bwa
+RUN wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR608/003/SRR6082043/SRR6082043_1.fastq.gz -O r1.fq.gz &&\
+wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR608/003/SRR6082043/SRR6082043_2.fastq.gz -O r2.fq.gz &&\
+wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/945/GCF_000006945.2_ASM694v2/GCF_000006945.2_ASM694v2_genomic.fna.gz &&\
+gunzip -c GCF_000006945.2_ASM694v2_genomic.fna.gz > ref.fa
+
+RUN bwa index ref.fa &&\
+bwa mem ref.fa r1.fq.gz r2.fq.gz > aln.sam &&\
+head aln.sam

polypolish/0.6.0-bwa/README.md

@@ -0,0 +1,42 @@
+# polypolish container
+
+Main tool: [polypolish](https://github.com/rrwick/Polypolish/wiki/How-to-run-Polypolish) v0.6.0
+
+Code repository: [polypolish](https://github.com/rrwick/Polypolish)
+
+Additional tools:
+
+- bwa: 0.7.18
+- python: 3.10
+
+Basic information on how to use this tool:
+
+- executable: polypolish
+- help: --help
+- version: --version
+- description: "Polypolish "polishes" consensus files created during assembly of long reads with Illumina short reads. Polypolish is a little different than other polishing tools in that paired-end reads need to be aligned separatly to generate two sam files."
+
+Additional information: This container also includes BWA v0.7.18 so that the user can align their short reads within the same container.
+
+Full documentation: [https://github.com/rrwick/Polypolish/wiki](https://github.com/rrwick/Polypolish/wiki)
+
+## Example Usage
+
+Use the included bwa software to align reads to the draft sequence. Please note that bbamp, minimap2 or any other similar software can perform a similar step that may be better suited for your use-case.
+
+```bash
+bwa index draft.fasta
+bwa mem -t 16 -a draft.fasta reads_1.fastq.gz > alignments_1.sam
+bwa mem -t 16 -a draft.fasta reads_2.fastq.gz > alignments_2.sam
+```
+
+Once the sam files are generated, they can be used with polypolish.
+
+```bash
+# paired end
+polypolish filter --in1 alignments_1.sam --in2 alignments_2.sam --out1 filtered_1.sam --out2 filtered_2.sam
+polypolish polish draft.fasta filtered_1.sam filtered_2.sam > polished.fasta
+
+# single end
+polypolish polish draft.fasta input.sam > polished.fasta
+```