Enabled installing gistic when directory already exists.

rules/GISTIC2.smk

 import datetime
+import os.path
 
 rule install_gistic:
     """Install GISTIC2 to a directory of choice."""
     output:
+        os.path.join(config["gisticdir"], "gistic2")
+    params:
         config["gisticdir"]
     shell:
-        "{workflow.basedir}/scripts/install_gistic2.sh {output}"
+        "{workflow.basedir}/scripts/install_gistic2.sh {params}"
 
 rule run_gistic:
     """Run GISTIC2 for the tumor segmentation data."""
     input:
-        gistic_directory=config["gisticdir"],
+        os.path.join(config["gisticdir"], "gistic2"),
         seg="Input/Segments_tumor.txt"
     output:
         "GISTIC/all_lesions.conf_" + config["gistic_precision"] + ".txt",