From a24cdc4e4381f92bbbcbfda30f1dcc54c8895cc4 Mon Sep 17 00:00:00 2001 From: Sarah Wait Zaranek Date: Tue, 7 Jul 2020 15:46:14 +0000 Subject: [PATCH] Updating bwa-samtools dockerfile Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek no issue # --- WGS-processing/docker/{bwa => bwa_samtools}/Dockerfile | 8 +++++--- WGS-processing/docker/clinvar-report/Dockerfile | 2 ++ 2 files changed, 7 insertions(+), 3 deletions(-) rename WGS-processing/docker/{bwa => bwa_samtools}/Dockerfile (76%) diff --git a/WGS-processing/docker/bwa/Dockerfile b/WGS-processing/docker/bwa_samtools/Dockerfile similarity index 76% rename from WGS-processing/docker/bwa/Dockerfile rename to WGS-processing/docker/bwa_samtools/Dockerfile index 7b13dd9..5f01b1d 100644 --- a/WGS-processing/docker/bwa/Dockerfile +++ b/WGS-processing/docker/bwa_samtools/Dockerfile @@ -15,8 +15,10 @@ RUN apt-get remove libhts-dev # 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 -# 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 samtools 1.10 +RUN wget https://github.com/samtools/samtools/archive/1.10.zip && unzip 1.10 && cd samtools-1.10 && 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 +RUN wget https://github.com/lh3/bwa/archive/v0.7.17.zip && unzip v0.7.17 && cd bwa-0.7.17 && make + +CMD /bin/sh diff --git a/WGS-processing/docker/clinvar-report/Dockerfile b/WGS-processing/docker/clinvar-report/Dockerfile index 8a93e4a..2c0976b 100644 --- a/WGS-processing/docker/clinvar-report/Dockerfile +++ b/WGS-processing/docker/clinvar-report/Dockerfile @@ -22,3 +22,5 @@ RUN cd /tmp && wget http://github.com/samtools/htslib/archive/1.10.2.zip && unzi # 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 + +CMD /bin/sh -- 2.30.2