updating biscuit version, adding flexbar and picard to container

Dockerfile

@@ -1,16 +1,54 @@
-FROM zhouwanding/biscuit_v0.3.8
+FROM ubuntu:latest
 MAINTAINER "Chris Miller" <[email protected]>
 
-####################
-#Biscuit QC scripts#
-####################
-RUN cd /opt && \
-    git clone https://github.com/zwdzwd/biscuit.git
-## Adding QC_scripts
-ADD Bisulfite_QC_bisulfiteconversion.sh /opt/biscuit/scripts
-ADD Bisulfite_QC_Coveragestats.sh /opt/biscuit/scripts
-ADD Bisulfite_QC_CpGretentiondistribution.sh /opt/biscuit/scripts
-ADD Bisulfite_QC_mappingsummary.sh /opt/biscuit/scripts
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update -y && \
+    apt-get install \
+    build-essential \
+    bzip2 \
+    cmake \
+    default-jre \
+    g++ \
+    git \
+    libbz2-dev \
+    liblzma-dev \
+    libncurses5 \
+    libtbb2 \
+    libtbb-dev \
+    make \
+    ncurses-dev \
+    wget \
+    xz-utils \
+    zlib1g-dev -y
+
+##################
+# Biscuit 0.3.16 #
+##################
+RUN mkdir /opt/biscuit_binary && cd /opt/biscuit_binary && \
+    wget https://github.com/huishenlab/biscuit/releases/download/v0.3.16.20200420/biscuit_0_3_16_linux_amd64 && \
+    chmod +x /opt/biscuit_binary/biscuit_0_3_16_linux_amd64 && \
+    ln -s /opt/biscuit_binary/biscuit_0_3_16_linux_amd64 biscuit && \
+    ln -s /opt/biscuit_binary/biscuit_0_3_16_linux_amd64 /usr/bin/biscuit
+
+###############
+# Flexbar 3.5 #
+###############
+
+RUN mkdir -p /opt/flexbar/tmp \
+    && cd /opt/flexbar/tmp \
+    && wget https://github.com/seqan/flexbar/archive/v3.5.0.tar.gz \
+    && wget https://github.com/seqan/seqan/releases/download/seqan-v2.4.0/seqan-library-2.4.0.tar.xz \
+    && tar xzf v3.5.0.tar.gz \
+    && tar xJf seqan-library-2.4.0.tar.xz \
+    && mv seqan-library-2.4.0/include flexbar-3.5.0 \
+    && cd flexbar-3.5.0 \
+    && cmake . \
+    && make \
+    && cp flexbar /opt/flexbar/ \
+    && cd / \
+    && rm -rf /opt/flexbar/tmp
+
 
 ##############
 #HTSlib 1.3.2#
@@ -25,6 +63,17 @@ RUN wget https://github.com/samtools/htslib/releases/download/1.3.2/htslib-1.3.2
     make install && \
     cp $HTSLIB_INSTALL_DIR/lib/libhts.so* /usr/lib/
 
+#################
+# Picard        #
+#################
+
+RUN mkdir /opt/picard-2.18.1/ \
+    && cd /tmp/ \
+    && wget --no-check-certificate https://github.com/broadinstitute/picard/releases/download/2.18.1/picard.jar \
+    && mv picard.jar /opt/picard-2.18.1/ \
+    && ln -s /opt/picard-2.18.1 /opt/picard \
+    && ln -s /opt/picard-2.18.1 /usr/picard
+
 #################
 #Sambamba v0.6.4#
 #################
@@ -41,43 +90,28 @@ RUN mkdir /opt/sambamba/ \
 #Samtools 1.3.1#
 ################
    ENV SAMTOOLS_INSTALL_DIR=/opt/samtools
-
-   WORKDIR /tmp
-   RUN wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 && \
-       tar --bzip2 -xf samtools-1.3.1.tar.bz2
-
-   WORKDIR /tmp/samtools-1.3.1
-   RUN ./configure --with-htslib=$HTSLIB_INSTALL_DIR --prefix=$SAMTOOLS_INSTALL_DIR && \
+   RUN cd /tmp && wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 && \
+       tar --bzip2 -xf samtools-1.3.1.tar.bz2 && cd /tmp/samtools-1.3.1 && \
+       ./configure --with-htslib=$HTSLIB_INSTALL_DIR --prefix=$SAMTOOLS_INSTALL_DIR && \
        make && \
-       make install
-
-   WORKDIR /
-   RUN rm -rf /tmp/samtools-1.3.1
-
-
-
-
+       make install && \
+       cd / && rm -rf /tmp/samtools-1.3.1 && ln -s /opt/samtools/bin/samtools /usr/bin/samtools
 
 ##########
 #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/*
+RUN mkdir /opt/bedtools && cd /opt/bedtools && wget https://github.com/arq5x/bedtools2/releases/download/v2.29.2/bedtools.static.binary && \
+    chmod +x /opt/bedtools/bedtools.static.binary && \
+    ln -s /opt/bedtools/bedtools.static.binary /usr/bin/bedtools
+
+####################
+#Biscuit QC scripts#
+####################
+RUN cd /opt && \
+    git clone https://github.com/zwdzwd/biscuit.git
+## Adding QC_scripts
+ADD Bisulfite_QC_bisulfiteconversion.sh /opt/biscuit/scripts
+ADD Bisulfite_QC_Coveragestats.sh /opt/biscuit/scripts
+ADD Bisulfite_QC_CpGretentiondistribution.sh /opt/biscuit/scripts
+ADD Bisulfite_QC_mappingsummary.sh /opt/biscuit/scripts