From 0e0c66c4d29041452975fca30e16e6e6db712fa5 Mon Sep 17 00:00:00 2001
From: Sarah Wait Zaranek <swz@curii.com>
Date: Tue, 23 Jun 2020 01:41:13 +0000
Subject: [PATCH] Updating clinvar report docker file and reorganizing yml
 files Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com> no
 issue #

---
 .../docker/clinvar-report/Dockerfile          | 53 +++----------------
 1 file changed, 8 insertions(+), 45 deletions(-)

diff --git a/WGS-processing/docker/clinvar-report/Dockerfile b/WGS-processing/docker/clinvar-report/Dockerfile
index 48d35df..8a93e4a 100644
--- a/WGS-processing/docker/clinvar-report/Dockerfile
+++ b/WGS-processing/docker/clinvar-report/Dockerfile
@@ -4,58 +4,21 @@ MAINTAINER Sarah Wait Zaranek <swz@curii.com>
 
 # Install python tools
 RUN apt-get update && apt-get install -y --no-install-recommends apt-utils
-RUN apt-get install -y apt-utils && apt-get install -y unzip
-RUN apt-get install autoconf -y 
-RUN apt-get install wget -y 
-RUN apt-get install python-pip -y
-RUN apt-get install python-numpy -y && apt-get install python-scipy -y
-RUN apt-get install python-matplotlib -y && apt-get install python-pandas -y
+RUN apt-get install -qy apt-utils unzip autoconf wget python-pip python-numpy python-scipy python-matplotlib python-pandas 
+
 RUN apt-get upgrade -y
 RUN apt-get clean
 
-# install lib files to build SAMtools
-RUN apt-get install libncurses5-dev -y && apt-get install libbz2-dev -y && apt-get install liblzma-dev -y && apt-get install git -y && apt-get install autoconf -y
-
-# installing zlib1g
-RUN apt-get install zlib1g-dev -y
-RUN apt-get install zlib1g -y
-
-# Installing xz-utils
-
-RUN apt-get install xz-utils -y
-
-# Installing liblzma-dev
-RUN apt-get install liblzma-dev -y
-
-# Installing pthreads
-RUN apt-get install libpthread-stubs0-dev -y
-
-# Installing libcurl
-RUN apt-get install libcurl3-openssl-dev -y
+# Install lib files to build SAMtools
+RUN apt-get install -qy libncurses5-dev libbz2-dev liblzma-dev git autoconf zlib1g-dev zlib1g xz-utils liblzma-dev libpthread-stubs0-dev 
+RUN apt-get install -qy libcurl3-openssl-dev libssl-dev bc build-essential parallel cmake 
 
-# Installing libcrypto
-RUN apt-get install libssl-dev -y
-
-# Installing bc
-RUN apt-get install bc -y
-
-# installing build essentials
-RUN apt-get install build-essential -y
-
-# Installing parallel
-RUN apt-get install parallel -y
-
-# Installing Cmake
-RUN apt-get install cmake -y
-
-# Installing SDSL
+# 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
 
-# Installing htslib
+# 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
 
-# Installing bcftools
-
+# 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
-- 
2.30.2