From 4306e9943b90a2adb4d19383a2caa1662a9e1d02 Mon Sep 17 00:00:00 2001
From: Sarah Wait Zaranek <swz@curii.com>
Date: Wed, 1 Apr 2020 03:40:07 +0000
Subject: [PATCH] updating dockerfiles Arvados-DCO-1.1-Signed-off-by: Sarah
 Wait Zaranek <swz@curii.com> no issue #

---
 docker/bam2fastq/Dockerfile      | 63 +++++++++++++++++++++++++++++---
 docker/clinvar-report/Dockerfile | 60 ++++++++++++++++++++++++++++++
 2 files changed, 118 insertions(+), 5 deletions(-)
 create mode 100644 docker/clinvar-report/Dockerfile

diff --git a/docker/bam2fastq/Dockerfile b/docker/bam2fastq/Dockerfile
index 86f399a..d40b3fa 100644
--- a/docker/bam2fastq/Dockerfile
+++ b/docker/bam2fastq/Dockerfile
@@ -1,10 +1,63 @@
-FROM arvados/jobs
-MAINTAINER Bryan Cosca <bcosca@curii.com>
-
+FROM arvados/jobs:latest
 USER root
 
-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 git
+# 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 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
+
+# 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
+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
+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 samtools
+
+RUN wget http://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2 && tar -xvf samtools-1.10.tar.bz2 && cd samtools-1.10 && autoheader && autoconf && ./configure && make && make install 
 
 RUN git clone --recursive https://github.com/jts/bam2fastq
 WORKDIR /bam2fastq
diff --git a/docker/clinvar-report/Dockerfile b/docker/clinvar-report/Dockerfile
new file mode 100644
index 0000000..d8811e0
--- /dev/null
+++ b/docker/clinvar-report/Dockerfile
@@ -0,0 +1,60 @@
+FROM arvados/jobs:latest
+USER root
+
+# 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 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
+
+# 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
+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
+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
+
+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