diff --git a/README.md b/README.md index 9b1c4ed2f..7e1fe9b94 100644 --- a/README.md +++ b/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/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bowtie2)](https://hub.docker.com/r/staphb/bowtie2) | | http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
https://github.com/BenLangmead/bowtie2 | | [Bracken](https://hub.docker.com/r/staphb/bracken/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bracken)](https://hub.docker.com/r/staphb/bracken) | | https://ccb.jhu.edu/software/bracken/index.shtml?t=manual
https://github.com/jenniferlu717/Bracken | | [BUSCO](https://hub.docker.com/r/staphb/busco/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/busco)](https://hub.docker.com/r/staphb/busco) | | https://busco.ezlab.org/busco_userguide.html
https://gitlab.com/ezlab/busco | -| [BWA](https://hub.docker.com/r/staphb/bwa)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bwa)](https://hub.docker.com/r/staphb/bwa) | | https://github.com/lh3/bwa | +| [BWA](https://hub.docker.com/r/staphb/bwa)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bwa)](https://hub.docker.com/r/staphb/bwa) | | https://github.com/lh3/bwa | | [Canu](https://hub.docker.com/r/staphb/canu)
[![docker pulls](https://badgen.net/docker/pulls/staphb/canu?)](https://hub.docker.com/r/staphb/canu)| | https://canu.readthedocs.io/en/latest/
https://github.com/marbl/canu | | [Canu-Racon](https://hub.docker.com/r/staphb/canu-racon/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/canu-racon)](https://hub.docker.com/r/staphb/canu-racon) | | https://canu.readthedocs.io/en/latest/
https://github.com/lbcb-sci/racon
https://github.com/isovic/racon (ARCHIVED)
https://lh3.github.io/minimap2/ | | [centroid](https://hub.docker.com/r/staphb/centroid/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/centroid)](https://hub.docker.com/r/staphb/centroid) | | https://github.com/stjacqrm/centroid | diff --git a/bwa/0.7.18/Dockerfile b/bwa/0.7.18/Dockerfile new file mode 100644 index 000000000..ed0b59ea7 --- /dev/null +++ b/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="kutluhan.incekara@ct.gov" + +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 \ No newline at end of file diff --git a/bwa/0.7.18/README.md b/bwa/0.7.18/README.md new file mode 100644 index 000000000..a332b8cfc --- /dev/null +++ b/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 +```