Merge branch 'dev' of ssh://git-r3lab-server.uni.lu:8022/shaman.narayanasamy/IMP into dev

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

@@ -466,9 +466,11 @@ rule ANALYSIS_VIZBIN:
         -k {config[vizbin][kmer]} \
         -p {config[vizbin][perp]} >> {log}
 
-        paste <(grep "^>" {output[0]} | sed -e 's/>//') \
-        <(cat $TMP_VIZBIN/data.points | sed -e 's/,/\t/') > {output[1]}
-
+        if [ -f $TMP_VIZBIN/data.points ]
+            then
+                paste <(grep "^>" {output[0]} | sed -e 's/>//') \
+                <(cat $TMP_VIZBIN/data.points | sed -e 's/,/\t/') > {output[1]}
+            fi
         rm -rf $TMP_VIZBIN
         """