From d210b46f9429aae64856dc52aec03040c0657b0e Mon Sep 17 00:00:00 2001
From: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
Date: Mon, 4 Nov 2019 16:26:00 -0500
Subject: [PATCH] Add bedr package to Docker and dependencies (#225)

* Add bedr package to Docker and dependencies

* Apparently bedr loading will mean the others installed properly

* Change zlib

* Comment on library(bedr)
---
 Dockerfile | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/Dockerfile b/Dockerfile
index d3ec2c098e..a74bc05f16 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -107,5 +107,41 @@ RUN apt-get update -qq && apt-get -y --no-install-recommends install \
     && install2.r --error \
     flextable
 
+# Required for mapping segments to genes
+# Add bedtools
+RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools-2.28.0.tar.gz
+RUN tar -zxvf bedtools-2.28.0.tar.gz
+RUN cd bedtools2 && \
+    make && \
+    mv bin/* /usr/local/bin
+
+# Required for installing htslib
+RUN apt-get update -qq && apt-get -y --no-install-recommends install \
+    zlib1g \
+    libbz2-dev \
+    liblzma-dev
+
+# Add bedops per the BEDOPS documentation
+RUN wget https://github.com/bedops/bedops/releases/download/v2.4.37/bedops_linux_x86_64-v2.4.37.tar.bz2
+RUN tar -jxvf bedops_linux_x86_64-v2.4.37.tar.bz2
+RUN cp bin/* /usr/local/bin
+
+# HTSlib
+RUN wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2
+RUN tar -jxvf htslib-1.9.tar.bz2
+RUN cd htslib-1.9 && \
+    ./configure && \
+    make && \
+    make install
+RUN mv bin/* /usr/local/bin
+
+# bedr package
+RUN apt-get update -qq && apt-get -y --no-install-recommends install \
+    && install2.r --error \
+    bedr
+
+# Check to make sure the binaries are available by loading the bedr library
+RUN Rscript -e "library(bedr)"
+
 #### Please install your dependencies here
 #### Add a comment to indicate what analysis it is required for