Merge pull request #968 from Kincekara/bwa

adds bwa 0.7.18

README.md

@@ -126,7 +126,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [bowtie2](https://hub.docker.com/r/staphb/bowtie2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bowtie2)](https://hub.docker.com/r/staphb/bowtie2) | <ul><li>[2.4.4](./bowtie2/2.4.4/)</li><li>[2.4.5](./bowtie2/2.4.5/)</li><li>[2.5.1](./bowtie2/2.5.1/)</li><li>[2.5.3](./bowtie2/2.5.3/)</li></ul> | http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml <br/>https://github.com/BenLangmead/bowtie2 |
 | [Bracken](https://hub.docker.com/r/staphb/bracken/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bracken)](https://hub.docker.com/r/staphb/bracken) | <ul><li>[2.9](./bracken/2.9)</li></ul> | https://ccb.jhu.edu/software/bracken/index.shtml?t=manual <br/>https://github.com/jenniferlu717/Bracken |
 | [BUSCO](https://hub.docker.com/r/staphb/busco/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/busco)](https://hub.docker.com/r/staphb/busco) | <ul><li>[5.4.7](./busco/5.4.7/)</li><li>[5.6.1](./busco/5.6.1/)</li><li>[5.6.1-prok-bacteria_odb10_2024-01-08](./busco/5.6.1-prok-bacteria_odb10_2024-01-08/)</li><li>[5.7.1](./busco/5.7.1/)</li><li>[5.7.1-prok-bacteria_odb10_2024-01-08](./busco/5.7.1-prok-bacteria_odb10_2024-01-08/)</li></ul> | https://busco.ezlab.org/busco_userguide.html <br/>https://gitlab.com/ezlab/busco |
-| [BWA](https://hub.docker.com/r/staphb/bwa) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bwa)](https://hub.docker.com/r/staphb/bwa) | <ul><li>0.7.17</li></ul> | https://github.com/lh3/bwa |
+| [BWA](https://hub.docker.com/r/staphb/bwa) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bwa)](https://hub.docker.com/r/staphb/bwa) | <ul><li>0.7.17</li><li>[0.7.18](./bwa/0.7.18/)</li></ul> | https://github.com/lh3/bwa |
 | [Canu](https://hub.docker.com/r/staphb/canu) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/canu?)](https://hub.docker.com/r/staphb/canu)| <ul><li>2.0</li><li>2.1.1</li><li>2.2</li></ul> | https://canu.readthedocs.io/en/latest/ <BR/> https://github.com/marbl/canu |
 | [Canu-Racon](https://hub.docker.com/r/staphb/canu-racon/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/canu-racon)](https://hub.docker.com/r/staphb/canu-racon) | <ul><li>1.7.1 (Canu), 1.3.1 (Racon), 2.13 (minimap2)</li><li>1.9 (Canu), 1.4.3 (Racon), 2.17 (minimap2)</li><li>1.9i (Canu), 1.4.3 (Racon), 2.17 (minimap2), (+racon_preprocess.py)</li><li>2.0 (Canu), 1.4.3 (Racon), 2.17 (minimap2)</li></ul> | https://canu.readthedocs.io/en/latest/ <br/> https://github.com/lbcb-sci/racon <br/> https://github.com/isovic/racon (ARCHIVED) <br/> https://lh3.github.io/minimap2/ |
 | [centroid](https://hub.docker.com/r/staphb/centroid/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/centroid)](https://hub.docker.com/r/staphb/centroid) | <ul><li>1.0.0</li></ul> | https://github.com/stjacqrm/centroid |

bwa/0.7.18/Dockerfile

@@ -0,0 +1,57 @@
+ARG BWA_VER=0.7.18
+
+## Builder ##
+FROM ubuntu:jammy as builder
+
+ARG BWA_VER
+
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    wget \
+    ca-certificates \
+    make \
+    gcc \
+    zlib1g-dev && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN wget https://github.com/lh3/bwa/archive/refs/tags/v${BWA_VER}.tar.gz &&\
+    tar -xvf v${BWA_VER}.tar.gz &&\
+    cd bwa-${BWA_VER} &&\
+    make &&\
+    mv bwa /usr/local/bin/
+
+## App ##
+FROM ubuntu:jammy as app 
+
+ARG BWA_VER
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="BWA"
+LABEL software.version="${BWA_VER}"
+LABEL description="Burrows-Wheeler Alignment Tool"
+LABEL website="https://github.com/lh3/bwa"
+LABEL license="https://github.com/lh3/bwa/blob/master/COPYING"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="[email protected]"
+
+COPY --from=builder /usr/local/bin/bwa /usr/local/bin/
+
+ENV LC_ALL=C
+
+CMD ["bwa"]
+
+WORKDIR /data
+
+## Test ##
+FROM app as test
+
+RUN apt-get update && apt-get install -y wget
+
+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

bwa/0.7.18/README.md

@@ -0,0 +1,30 @@
+# BWA container
+
+Main tool: [bwa](https://bio-bwa.sourceforge.net/)
+
+Code repository: https://github.com/lh3/bwa
+
+Basic information on how to use this tool:
+
+- executable: bwa
+- description: Burrows-Wheeler Aligner
+
+Full documentation: https://bio-bwa.sourceforge.net/
+
+## Example Usage
+
+```bash
+# Illumina/454/IonTorrent single-end reads longer than ~70bp
+bwa mem ref.fa reads.fq > aln.sam
+# Illumina single-end reads shorter than ~70bp:
+bwa aln ref.fa reads.fq > reads.sai
+bwa samse ref.fa reads.sai reads.fq > aln-se.sam
+# Illumina/454/IonTorrent paired-end reads longer than ~70bp:
+bwa mem ref.fa read1.fq read2.fq > aln-pe.sam
+# Illumina paired-end reads shorter than ~70bp:
+bwa aln ref.fa read1.fq > read1.sai; bwa aln ref.fa read2.fq > read2.sai
+bwa sampe ref.fa read1.sai read2.sai read1.fq read2.fq > aln-pe.sam
+# PacBio subreads or Oxford Nanopore reads to a reference genome:
+bwa mem -x pacbio ref.fa reads.fq > aln.sam
+bwa mem -x ont2d ref.fa reads.fq > aln.sam
+```