Move docker image back to openjdk:8u121 so bowtie build works

Also split bwa tools out into own dockerfile to keep things simple

Dockerfile

@@ -1,4 +1,5 @@
-FROM openjdk:8
+# openjdk:8 moved from debian jessie to stretch after u131, which breaks everything (bowtie)
+FROM openjdk:8u121
 
 LABEL authors="[email protected],[email protected]" \
     description="Docker image containing all requirements for NGI-MethylSeq pipeline"
@@ -52,12 +53,6 @@ RUN curl -fsSL https://github.com/samtools/samtools/releases/download/1.5/samtoo
     make install && \
     rm /opt/samtools-1.5.tar.bz2
 
-# Install PicardTools
-RUN curl -fsSL https://github.com/broadinstitute/picard/releases/download/2.0.1/picard-tools-2.0.1.zip -o /opt/picard-tools-2.0.1.zip && \
-    unzip /opt/picard-tools-2.0.1.zip -d /opt/ && \
-    rm /opt/picard-tools-2.0.1.zip
-ENV PICARD_HOME /opt/picard-tools-2.0.1
-
 # Install Bowtie2
 RUN mkdir /opt/bowtie2 && \
     curl -fsSL https://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.2/bowtie2-2.3.2-source.zip -o /opt/bowtie2/bowtie2.zip && \
@@ -82,27 +77,5 @@ RUN mkdir /opt/Qualimap && \
     ln -s /opt/Qualimap/qualimap_v2.2.1/qualimap /usr/local/bin/qualimap && \
     rm /opt/Qualimap/qualimap.zip
 
-# Install BWA
-RUN mkdir /opt/bwa && \
-    curl -fsSL https://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.15.tar.bz2 -o /opt/bwa/bwa.tar.bz2 && \
-    tar xvjf /opt/bwa/bwa.tar.bz2 -C /opt/bwa/ && \
-    cd /opt/bwa/bwa-0.7.15/ && \
-    make && \
-    ln -s /opt/bwa/bwa-0.7.15/bwa /usr/local/bin/bwa && \
-    rm /opt/bwa/bwa.tar.bz2
-
-# Install bwa-meth
-RUN pip install toolshed && \
-    pip install git+git://github.com/brentp/bwa-meth.git
-
-# Install MethylDackel
-RUN mkdir /opt/MethylDackel && \
-    curl -fsSL https://github.com/dpryan79/MethylDackel/archive/0.2.1.zip -o /opt/MethylDackel/MethylDackel.zip && \
-    unzip /opt/MethylDackel/MethylDackel.zip -d /opt/MethylDackel && \
-    cd /opt/MethylDackel/MethylDackel-0.2.1 && \
-    make && \
-    make install prefix=/usr/local/bin && \
-    rm /opt/MethylDackel/MethylDackel.zip
-
 # Install MultiQC
-RUN pip install multiqc
+RUN pip install git+https://github.com/ewels/MultiQC.git

Dockerfile-bwa

@@ -0,0 +1,91 @@
+FROM openjdk:8
+
+LABEL authors="[email protected],[email protected]" \
+    description="Docker image containing all requirements for NGI-MethylSeq pipeline"
+
+# Install container-wide requrements gcc, pip, zlib, libssl, make, libncurses, fortran77, g++, R
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+        g++ \
+        gcc \
+        gfortran \
+        libbz2-dev \
+        libcurl4-openssl-dev \
+        libgsl0-dev \
+        liblzma-dev \
+        libncurses5-dev \
+        libpcre3-dev \
+        libreadline-dev \
+        libssl-dev \
+        libtbb-dev \
+        make \
+        python-dev \
+        zlib1g-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install pip
+RUN curl -fsSL https://bootstrap.pypa.io/get-pip.py -o /opt/get-pip.py && \
+    python /opt/get-pip.py && \
+    rm /opt/get-pip.py
+
+RUN curl -fsSL http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip -o /opt/fastqc_v0.11.5.zip && \
+    unzip /opt/fastqc_v0.11.5.zip -d /opt/ && \
+    chmod 755 /opt/FastQC/fastqc && \
+    ln -s /opt/FastQC/fastqc /usr/local/bin/fastqc && \
+    rm /opt/fastqc_v0.11.5.zip
+
+# Install cutadapt
+RUN pip install cutadapt
+
+# Install TrimGalore
+RUN mkdir /opt/TrimGalore && \
+    curl -fsSL https://github.com/FelixKrueger/TrimGalore/archive/0.4.4.zip -o /opt/TrimGalore/0.4.4.zip && \
+    unzip /opt/TrimGalore/0.4.4.zip -d /opt/TrimGalore && \
+    ln -s /opt/TrimGalore/TrimGalore-0.4.4/trim_galore /usr/local/bin/trim_galore && \
+    rm /opt/TrimGalore/0.4.4.zip
+
+# Install SAMTools
+RUN curl -fsSL https://github.com/samtools/samtools/releases/download/1.5/samtools-1.5.tar.bz2 -o /opt/samtools-1.5.tar.bz2 && \
+    tar xvjf /opt/samtools-1.5.tar.bz2 -C /opt/ && \
+    cd /opt/samtools-1.5 && \
+    make && \
+    make install && \
+    rm /opt/samtools-1.5.tar.bz2
+
+# Install PicardTools
+RUN curl -fsSL https://github.com/broadinstitute/picard/releases/download/2.0.1/picard-tools-2.0.1.zip -o /opt/picard-tools-2.0.1.zip && \
+    unzip /opt/picard-tools-2.0.1.zip -d /opt/ && \
+    rm /opt/picard-tools-2.0.1.zip
+ENV PICARD_HOME /opt/picard-tools-2.0.1
+
+# Install Qualimap
+RUN mkdir /opt/Qualimap && \
+    curl -fsSL https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.2.1.zip -o /opt/Qualimap/qualimap.zip && \
+    unzip /opt/Qualimap/qualimap.zip -d /opt/Qualimap && \
+    ln -s /opt/Qualimap/qualimap_v2.2.1/qualimap /usr/local/bin/qualimap && \
+    rm /opt/Qualimap/qualimap.zip
+
+# Install BWA
+RUN mkdir /opt/bwa && \
+    curl -fsSL https://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.15.tar.bz2 -o /opt/bwa/bwa.tar.bz2 && \
+    tar xvjf /opt/bwa/bwa.tar.bz2 -C /opt/bwa/ && \
+    cd /opt/bwa/bwa-0.7.15/ && \
+    make && \
+    ln -s /opt/bwa/bwa-0.7.15/bwa /usr/local/bin/bwa && \
+    rm /opt/bwa/bwa.tar.bz2
+
+# Install bwa-meth
+RUN pip install toolshed && \
+    pip install git+git://github.com/brentp/bwa-meth.git
+
+# Install MethylDackel
+RUN mkdir /opt/MethylDackel && \
+    curl -fsSL https://github.com/dpryan79/MethylDackel/archive/0.2.1.zip -o /opt/MethylDackel/MethylDackel.zip && \
+    unzip /opt/MethylDackel/MethylDackel.zip -d /opt/MethylDackel && \
+    cd /opt/MethylDackel/MethylDackel-0.2.1 && \
+    make && \
+    make install prefix=/usr/local/bin && \
+    rm /opt/MethylDackel/MethylDackel.zip
+
+# Install MultiQC
+RUN pip install multiqc