Use picard command instead of jar

snakecnv/referencebundle.snk

@@ -27,8 +27,6 @@ WDIR = config['workdir']
 
 workdir: WDIR
 
-PicardJar="/usr/local/bioinfo/src/picard-tools/current/picard.jar"
-
 # Always set the environment
 
 shell.prefix("export PATH={root_dir}/bin:{sv_dir}/bwa:\"$PATH\"; export LD_LIBRARY_PATH={sv_dir}/bwa:/SGE/ogs/lib/linux-x64:\"$LD_LIBRARY_PATH\"; ".format(
@@ -219,7 +217,7 @@ rule dict:
     output:
         PREFIX+".dict"
     shell:
-        "java -jar {PicardJar} CreateSequenceDictionary "
+        "picard CreateSequenceDictionary "
         " R= {input} "
         " O= {output} "