diff --git a/rules/Util.rules b/rules/Util.rules index 12880b10f1bdcc0c1962018ff16c5e4f0ad0bf2e..8a789775918fc4e2c032737a2228f911f18efbe8 100644 --- a/rules/Util.rules +++ b/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 """