Merge pull request #79 from sanger-pathogens/add_dockerfile

Dockerfile: peg samtools version and downgrade to 0.1.19

Dockerfile

@@ -3,11 +3,15 @@ FROM ubuntu:18.04
 ARG   DEBIAN_FRONTEND=noninteractive
 ARG   BUILD_DIR=/opt/fastaq
 
+ARG   SAMTOOLS_VERSION=0.1.19
+ENV   SAMTOOLS_URL=https://github.com/samtools/samtools/archive/${SAMTOOLS_VERSION}.tar.gz
+ENV   SAMTOOLS_DIR=/usr/local/samtools-${SAMTOOLS_VERSION}
+
 # Install the dependancies
 RUN   apt-get update && \
       apt-get install --yes apt-utils && \
       apt-get --yes upgrade && \
-      apt-get install --yes python3 python3-pip samtools
+      apt-get install --yes curl python3 python3-pip
 
 RUN   apt-get install -y locales && \
       sed -i -e 's/# \(en_GB\.UTF-8 .*\)/\1/' /etc/locale.gen && \
@@ -17,8 +21,27 @@ ENV   LANG     en_GB.UTF-8
 ENV   LANGUAGE en_GB:en
 ENV   LC_ALL   en_GB.UTF-8
 
-COPY  . ${BUILD_DIR}
+# samtools build
+# nore specific version requirement
+RUN   apt-get install --yes libncurses5-dev libz-dev
+RUN   mkdir -p ${SAMTOOLS_DIR} && \
+      cd ${SAMTOOLS_DIR} && \
+      curl -fsSL ${SAMTOOLS_URL} | tar xzf - --strip-components=1 && \
+      echo -n "Building samtools... " && \
+      make > make.log 2>&1; \
+      EXIT=$?; \
+      if [ $? -ne ${EXIT} ]; then echo "FAILED:" && cat make.log && exit ${EXIT}; else echo "OK."; fi
+ENV   PATH ${SAMTOOLS_DIR}:${SAMTOOLS_DIR}/misc:${PATH}
+
+# check samtools is an executable in the path
+RUN   samtools 2> /tmp/samtools.out; \
+      EXIT=$?; \
+      if [ 1 -ne ${EXIT} ]; then \
+         cat /tmp/samtools.out && exit ${EXIT}; \
+      fi;
 
+# Fastaq build
+COPY  . ${BUILD_DIR}
 RUN   cd ${BUILD_DIR} && \
       python3 setup.py test && \
       python3 setup.py install && \

README.md

@@ -46,7 +46,7 @@ The test can be run from the top level directory:
 ### Runtime dependencies
 
 These must be available in your path at run time:
-  * samtools
+  * samtools 0.1.19
   * gzip
   * gunzip