From 7e3dd4a087bf43c783e329220a236701eedd955a Mon Sep 17 00:00:00 2001
From: Sai Mukund Ramakrishnan
 <saimukund@timothys-mbp.wusm-wifi.wucon.wustl.edu>
Date: Tue, 9 Apr 2019 13:22:55 -0500
Subject: [PATCH] Adding bedtools and the Biscuit shell scripts

---
 Dockerfile | 31 ++++++++++++++++++++++++++++++-
 1 file changed, 30 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index ea1a1c4..4d0674d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,11 +1,16 @@
 FROM zhouwanding/biscuit_v0.3.8
 MAINTAINER "Chris Miller" <c.a.miller@wustl.edu>
 
+####################
+#Biscuit QC scripts#
+####################
+RUN cd /opt && \
+    git clone https://github.com/zwdzwd/biscuit.git
+
 ##############
 #HTSlib 1.3.2#
 ##############
 ENV HTSLIB_INSTALL_DIR=/opt/htslib
-
 WORKDIR /tmp
 RUN wget https://github.com/samtools/htslib/releases/download/1.3.2/htslib-1.3.2.tar.bz2 && \
     tar --bzip2 -xvf htslib-1.3.2.tar.bz2 && \
@@ -26,3 +31,27 @@ RUN mkdir /opt/sambamba/ \
    ADD sambamba_merge /usr/bin/
    RUN chmod +x /usr/bin/sambamba_merge
 
+
+##########
+#Bedtools#
+##########
+
+ARG PACKAGE_VERSION=2.27.1
+ARG BUILD_PACKAGES="git openssl python build-essential zlib1g-dev"
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update && \
+    apt-get install --yes \
+              $BUILD_PACKAGES && \
+    cd /tmp && \
+    git clone https://github.com/arq5x/bedtools2.git && \
+    cd bedtools2 && \
+    git checkout v$PACKAGE_VERSION && \
+    make && \
+    mv bin/* /usr/local/bin && \
+    cd / && \
+    rm -rf /tmp/* && \
+    apt remove --purge --yes \
+              $BUILD_PACKAGES && \
+    apt autoremove --purge --yes && \
+    apt clean && \
+    rm -rf /var/lib/apt/lists/*
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