From: Sarah Wait Zaranek Date: Tue, 23 Jun 2020 17:15:13 +0000 (+0000) Subject: Adding changes to Dockerfiles X-Git-Url: https://git.arvados.org/arvados-tutorial.git/commitdiff_plain/affbf1f65ecfe64c76080207a2ae2f59389b50e4 Adding changes to Dockerfiles Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek no issue # --- diff --git a/WGS-processing/docker/bwa/Dockerfile b/WGS-processing/docker/bwa/Dockerfile index 94254dd..7b13dd9 100644 --- a/WGS-processing/docker/bwa/Dockerfile +++ b/WGS-processing/docker/bwa/Dockerfile @@ -3,20 +3,20 @@ USER root MAINTAINER Sarah Wait Zaranek RUN apt-get update -qy -RUN apt-get install -qy build-essential wget cmake zlib1g-dev python-pip unzip libbz2-dev liblzma-dev libcurl4-openssl-dev libncurses-dev +RUN apt-get install -qy build-essential wget cmake zlib1g-dev python-pip unzip libbz2-dev liblzma-dev libcurl4-openssl-dev libncurses-dev autoconf git RUN mkdir -p /usr/share/man/man1 RUN apt-get install -qy default-jdk -ADD bwa-0.7.17.tar.bz2 / -WORKDIR bwa-0.7.17 -RUN make +# Install SDSL +RUN cd /tmp && git clone 'https://github.com/simongog/sdsl-lite.git' && cd sdsl-lite && ./install.sh /usr/local +RUN apt-get remove libhts-dev -ADD samtools-1.10.tar.bz2 / -WORKDIR /samtools-1.10 -RUN ./configure && make && make install +# Install htslib 1.10.2 +RUN cd /tmp && wget http://github.com/samtools/htslib/archive/1.10.2.zip && unzip 1.10.2 && cd htslib-1.10.2 && make && make install && cd /tmp && rm -rf htslib-1.10.2 && ldconfig -ADD picard.jar / - -WORKDIR / +# Install bcftools 1.10.2 +RUN wget http://github.com/samtools/bcftools/archive/1.10.2.zip && unzip 1.10.2 && cd bcftools-1.10.2 && autoheader && autoconf && ./configure && make && make install +# Install BWA 07.7.17 +RUN wget https://github.com/lh3/bwa/archive/v0.7.17.zip && unzip v0.7.17 && cd bwa-0.7.17 && make