BWA + Samtools to allow piping between bwa mem and samtools view
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For workflows, instead of having two steps (where BWA mem can produce SAM files that are terabytes), pipe it directly to samtools view.
In the version tag, the first is the BWA version, the second is the Samtools version. Eg: 0.7.17-1.9 is BWA (0.7.17) and Samtools (1.9). These were the most up to date version when this was published (2019-05-09).
Dockerfile:
# Merge BWA and SAMTOOLS together to allow us to pipe bwa mem to samtools view
FROM ubuntu:16.04
RUN apt-get update -qq \
&& apt-get install -qq bzip2 gcc g++ make zlib1g-dev wget libncurses5-dev liblzma-dev libbz2-dev
ENV BWA_VERSION 0.7.17
ENV SAMTOOLS_VERSION 1.9
RUN cd /opt/ \
&& wget https://github.com/lh3/bwa/releases/download/v${BWA_VERSION}/bwa-${BWA_VERSION}.tar.bz2 \
&& tar -xjf bwa-${BWA_VERSION}.tar.bz2 \
&& rm -f bwa-${BWA_VERSION}.tar.bz2 \
&& cd /opt/bwa-${BWA_VERSION}/ \
&& make
RUN cd /opt/ \
&& wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 \
&& tar -xjf samtools-${SAMTOOLS_VERSION}.tar.bz2 \
&& rm -rf samtools-${SAMTOOLS_VERSION}.tar.bz2 \
&& cd samtools-${SAMTOOLS_VERSION}/ \
&& make && make install
ENV PATH="/opt/bwa-${BWA_VERSION}/:/opt/samtools-${SAMTOOLS_VERSION}/:${PATH}"
Content type
Image
Digest
Size
162.1 MB
Last updated
almost 7 years ago
docker pull michaelfranklin/bwasamtools:0.7.17-1.10