Add samtools to Dockerfile

Dockerfile

@@ -3,7 +3,9 @@ MAINTAINER [email protected]
 
 # Install prerequisites
 RUN apt update && \
-	apt-get install -y build-essential wget unzip python2.7 python-dev git python-pip bats awscli curl
+	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
+
 
 # Use /share as the working directory
 RUN mkdir /share
@@ -26,11 +28,23 @@ ENV PYTHONPATH="/usr/midas/MIDAS-1.3.2:${PYTHONPATH}"
 ENV PATH="/usr/midas/MIDAS-1.3.2/bin/Linux:${PATH}"
 ENV PATH="/usr/midas/MIDAS-1.3.2/scripts:${PATH}"
 
+# Install SAMTOOLS
+RUN 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 && \
+	./configure --without-curses && \
+	make && \
+	make install && \
+	rm /usr/local/bin/samtools && \
+	rm /usr/midas/MIDAS-1.3.2/bin/Linux/samtools && \
+	ln -s /usr/midas/samtools-1.4/samtools /usr/local/bin/ && \
+	rm /usr/midas/samtools-1.4.tar.bz2
 
 # Install the SRA toolkit
 RUN 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 xzvf 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
 

tests/tests.bats

@@ -17,6 +17,12 @@
   [[ "$v" =~ "7.47.0" ]]
 }
 
+@test "Samtools v1.4" {
+  v="$(samtools --version)"
+
+  [[ "$v" =~ "samtools 1.4" ]]
+}
+
 @test "Make sure MIDAS is in the PATH" {
   h="$(run_midas.py -h)"