add docker Entrypoint

docker/Dockerfile

@@ -214,6 +214,7 @@ RUN echo "`snakemake --bash-completion`" >> ~/.bashrc \
 ######################
 ENV PATH /home/imp/lib/trinityrnaseq_r20140717:/home/imp/lib/Platypus_0.8.1:/home/imp/lib/megahit:$PATH
 
-VOLUME ["/shared"]
+VOLUME ["/data", "/config"]
 WORKDIR /home/imp/integrated-metaomic-pipeline
-CMD ["/bin/bash"]
+ENTRYPOINT ["snakemake"]
+CMD ["ALL"]

rules/Analysis/MGMT.rules

@@ -465,7 +465,7 @@ rule ANALYSIS_VIZBIN:
         -o $TMP_VIZBIN/data.points \
         -k {config[vizbin][kmer]} \
         -p {config[vizbin][perp]} >> {log}
-
+        echo rv: $?
         paste <(grep "^>" {output[0]} | sed -e 's/>//') \
         <(cat $TMP_VIZBIN/data.points | sed -e 's/,/\t/') > {output[1]}