Refactored Dockerfile to make image smaller

Dockerfile

@@ -1,5 +1,4 @@
-
-FROM pditommaso/dkrbase
+FROM pditommaso/dkrbase:1.2
 MAINTAINER Maria Chatzou <mxatzou@gmail.com>
 
 
@@ -9,63 +8,44 @@ RUN apt-get update -y --fix-missing && apt-get install -y \
     libargtable2-dev
 
 
-#RUN git clone https://github.com/cbcrg/shootstrap.git
-#RUN cd shootstrap \
-#    cp bin/* ../ \
-#    cd ..
-
-
 #
-# Get and compile T-Coffee
+# Download T-Coffee pre-built package
 #
 RUN wget -q http://www.tcoffee.org/Packages/Stable/Version_11.00.8cbe486/linux/T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.tar.gz && \
   tar xf T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.tar.gz && \
   mv T-COFFEE_installer_Version_11.00.8cbe486_linux_x64 /opt/tcoffee && \
   rm -rf T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.tar.gz
 
-ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/blast/bin:/opt/sate/sate-core/bin:/opt/tcoffee/bin:/opt/tcoffee/plugins/linux/
-ENV TEMP /tmp
-ENV DIR_4_TCOFFEE /opt/tcoffee
-ENV EMAIL_4_TCOFFEE tcoffee.msa@gmail.com
-ENV CACHE_4_TCOFFEE /tmp/cache/
-ENV LOCKDIR_4_TCOFFEE /tmp/lck/
-ENV TMP_4_TCOFFEE /tmp/tmp/  
+ENV PATH=$PATH:/opt/tcoffee/bin:/opt/tcoffee/plugins/linux/ TEMP=/tmp DIR_4_TCOFFEE=/opt/tcoffee EMAIL_4_TCOFFEE=tcoffee.msa@gmail.com CACHE_4_TCOFFEE=/tmp/cache/ LOCKDIR_4_TCOFFEE=/tmp/lck/ TMP_4_TCOFFEE=/tmp/tmp/  
 
 
 #
 # Get and compile ClustalO
 #
-RUN wget http://www.clustal.org/omega/clustal-omega-1.2.1.tar.gz
-RUN tar -xvzf clustal-omega-1.2.1.tar.gz
-RUN cd clustal-omega-1.2.1 &&\
-    ./configure &&\
-    make &&\
-    cp src/clustalo /usr/local/bin/    
-    #mv ../exe/seqboot /usr/local/bin/
-
+RUN wget http://www.clustal.org/omega/clustal-omega-1.2.1.tar.gz -q -O- | tar -xz &&\
+  cd clustal-omega-1.2.1 &&\
+  ./configure &&\
+  make &&\
+  cp src/clustalo /usr/local/bin/ &&\
+  rm -rf /clustal-omega-1.2.1   
 
 
 #
 # Get and compile FastTree
 #
-RUN mkdir FastTree_dir
-RUN cd FastTree_dir
-RUN wget http://meta.microbesonline.org/fasttree/FastTree.c
-RUN gcc -O3 -finline-functions -funroll-loops -Wall -o FastTree FastTree.c -lm
-RUN mv FastTree /usr/local/bin/
-RUN cd ..
-
-#ENTRYPOINT ["/usr/local/bin/FastTree"]
+RUN mkdir FastTree_dir &&\
+ cd FastTree_dir &&\
+ wget http://meta.microbesonline.org/fasttree/FastTree.c -q &&\
+ gcc -O3 -finline-functions -funroll-loops -Wall -o FastTree FastTree.c -lm &&\
+ mv FastTree /usr/local/bin/ &&\
+ rm -rf /FastTree_dir
 
 #
 # Get and compile SeqBoot
 #
-RUN wget http://evolution.gs.washington.edu/phylip/download/phylip-3.696.tar.gz
-RUN tar -xvzf phylip-3.696.tar.gz
-RUN cd phylip-3.696/src \
-    Makefile.unx Makefile \
-    make install \
-    mv ../exe/seqboot /usr/local/bin/
-
-#ENTRYPOINT ["/usr/local/bin/seqboot"]
+RUN wget http://evolution.gs.washington.edu/phylip/download/phylip-3.696.tar.gz -q -O- | tar -xz &&\
+ cd phylip-3.696/src &&\
+ make -f Makefile.unx install &&\
+ mv ../exe/seqboot /usr/local/bin/ &&\
+ rm -rf /phylip-3.696
 

nextflow.config

@@ -4,5 +4,5 @@ manifest {
 }
 
 process { 
-  container = 'cbcrg/shootstrap-nf' 
+  container = 'cbcrg/shootstrap-nf@sha256:e12a0c250efe3a9ee46dab86b38ca96c2b1f2b063c2276a4ebd4fa5048e1fa3b' 
 }