Install as much as possible in a single layer

Dockerfile

@@ -7,31 +7,26 @@ ADD requirements.txt /usr/midas
 
 
 # Install prerequisites
+# Install MIDAS, and remove the samtools and bowtie2 binaries
+# Install Samtools
+# Install Bowtie2
+# Install SRA toolkit
 RUN apt update && \
 	apt-get install -y build-essential wget unzip python2.7 python-dev git python-pip \
 	bats awscli curl zlib1g-dev libbz2-dev liblzma-dev libcurl4-openssl-dev libssl1.0.0 \
 	libssl-dev libtbb-dev g++ && \
-	pip install -r /usr/midas/requirements.txt
-
-
-# Use /share as the working directory
-RUN mkdir /share
-WORKDIR /share
-
-
-# Install MIDAS and remove the samtools and bowtie2 binaries
-RUN cd /usr/midas && \
+	pip install -r /usr/midas/requirements.txt && \
+	cd /usr/midas && \
+	echo "" && \
+	echo "INSTALLING MIDAS" && \
 	wget https://github.com/snayfach/MIDAS/archive/v1.3.2.tar.gz && \
 	tar xzf v1.3.2.tar.gz && \
 	python MIDAS-1.3.2/setup.py install && \
 	rm /usr/midas/MIDAS-1.3.2/bin/Linux/samtools && \
-	rm /usr/midas/MIDAS-1.3.2/bin/Linux/bowtie2*	
-# Add to the PATH
-ENV PYTHONPATH="/usr/midas/MIDAS-1.3.2:${PYTHONPATH}"
-ENV PATH="/usr/midas/MIDAS-1.3.2/scripts:${PATH}"
-
-# Install SAMTOOLS
-RUN cd /usr/midas && \
+	rm /usr/midas/MIDAS-1.3.2/bin/Linux/bowtie2* && \
+	echo "" && \
+	echo "INSTALLING SAMTOOLS" && \
+	cd /usr/midas && \
 	wget https://github.com/samtools/samtools/releases/download/1.4/samtools-1.4.tar.bz2 && \
 	tar xf samtools-1.4.tar.bz2 && \
 	cd samtools-1.4 && \
@@ -41,24 +36,32 @@ RUN cd /usr/midas && \
 	rm /usr/local/bin/samtools && \
 	ln -s /usr/midas/samtools-1.4/samtools /usr/midas/MIDAS-1.3.2/bin/Linux/ && \
 	ln -s /usr/midas/samtools-1.4/samtools /usr/local/bin/ && \
-	rm /usr/midas/samtools-1.4.tar.bz2
-
-# Install Bowtie2
-RUN cd /usr/midas && \
+	rm /usr/midas/samtools-1.4.tar.bz2 && \
+	echo "" && \
+	echo "INSTALLING BOWTIE2" && \
+	cd /usr/midas && \
 	wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.2/bowtie2-2.3.2-linux-x86_64.zip && \
 	unzip bowtie2-2.3.2-linux-x86_64.zip && \
 	rm bowtie2-2.3.2-linux-x86_64.zip && \
 	cd bowtie2-2.3.2 && \
 	ln -s /usr/midas/bowtie2-2.3.2/bowtie2* /usr/midas/MIDAS-1.3.2/bin/Linux/ && \
-	ln -s /usr/midas/bowtie2-2.3.2/bowtie2* /usr/local/bin/
-
-# Install the SRA toolkit
-RUN cd /usr/local/bin && \
+	ln -s /usr/midas/bowtie2-2.3.2/bowtie2* /usr/local/bin/ && \
+	echo "" && \
+	echo "INSTALLING SRA TOOLKIT" && \
+	cd /usr/local/bin && \
 	wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.8.2/sratoolkit.2.8.2-ubuntu64.tar.gz && \
 	tar xzf sratoolkit.2.8.2-ubuntu64.tar.gz && \
 	ln -s /usr/local/bin/sratoolkit.2.8.2-ubuntu64/bin/* /usr/local/bin/ && \
 	rm sratoolkit.2.8.2-ubuntu64.tar.gz
 
+# Use /share as the working directory
+RUN mkdir /share
+WORKDIR /share
+
+# Add to the PATH
+ENV PYTHONPATH="/usr/midas/MIDAS-1.3.2:${PYTHONPATH}"
+ENV PATH="/usr/midas/MIDAS-1.3.2/scripts:${PATH}"
+
 # Add the run script to the PATH
 ADD run.py /usr/midas
 ADD helpers /usr/midas/helpers
@@ -67,10 +70,6 @@ RUN cd /usr/midas && \
 	ln -s /usr/midas/run.py /usr/bin/
 
 
-# Install prereq's including Numpy a second time
-RUN pip install -r /usr/midas/requirements.txt
-
-
 # Run tests and then remove the folder
 ADD tests /usr/midas/tests
 RUN bats /usr/midas/tests/ && rm -r /usr/midas/tests/