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

rules/Util.rules

@@ -226,14 +226,15 @@ rule _DOWNLOAD_KEGG_INFORMATION:
     benchmark:
         "%s/benchmarks/DOWNLOAD_KEGG_INFORMATION.json" % U_OUT
     output:
-        "%s/ec2pathway.txt" % DBPATH
+        "%s/ec2pathway.txt" % DBPATH,
+        "%s/pathway2hierarchy.txt" % DBPATH
     shell:
         """
         wget --no-check-certificate {config[kegg][db_ec2pthy]} -O {DBPATH}/ec2pathway.txt.tmp
-        grep "path:ec" {DBPATH}/ec2pathway.txt.tmp | sed -e 's/path:ec//g' | sed -e 's/ec://g' > {DBPATH}/ec2pathway.txt
+        grep "path:ec" {DBPATH}/ec2pathway.txt.tmp | sed -e 's/path:ec//g' | sed -e 's/ec://g' > {output[0]}
         rm {DBPATH}/ec2pathway.txt.tmp
 
         wget --no-check-certificate {config[kegg][db_hierarchy]} -O {DBPATH}/pathway2hierarchy.txt.tmp
-        cat {DBPATH}/pathway2hierarchy.txt.tmp | sed -e 's/path:map//g'  > {DBPATH}/pathway2hierarchy.txt
+        cat {DBPATH}/pathway2hierarchy.txt.tmp | sed -e 's/path:map//g'  > {output[1]}
         rm {DBPATH}/pathway2hierarchy.txt.tmp
         """