Updating bwa-samtools dockerfile

Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

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 7b13dd9b46d0ebdceffb5e98f2108e5bd70c832f..5f01b1dea744d7ce3bb635caeade28dd70b97ed3 100644 (file)
--- 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 8a93e4a2b80c0e1d48fd5760842d20cd1331c54b..2c0976b87205fdec28a3c3d0e105fa7cf5181ac5 100644 (file)
--- 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