Updated sample size test.

config.yaml

 #Directories to be specified
 workdir: /home/bftan/CNA_results        #directory to write output
-gisticdir: /home/bftan/Tools/GISTIC2_test    #directory to install GISTIC2
+gisticdir: /home/bftan/Tools/GISTIC2    #directory to install GISTIC2
 
 #workdir: /home/bftan/CNA_results        #directory to write output
 #gisticdir: /home/bftan/Tools/GISTIC2    #directory to install GISTIC2

rules/SampleSizes.smk

 import ReportSizes
 from SampleSizes import SegFile
-from Rubic import MarkerFile
+import os.path
+import datetime
 
 rule seg_subsets:
     """Create segmentation files with different numbers of samples (randomly chosen) for a number of times."""
@@ -14,10 +15,10 @@ rule seg_subsets:
 rule run_gistic_subsets:
     """Run GISTIC2 for the segmentation files with different subsets."""
     input:
-        gistic_directory=config["gisticdir"],
+        gistic_directory=os.path.join(config["gisticdir"], "gistic2"),
         seg="Samplesize/Input/Size{rand_nr}.Rep{rep_nr}.txt"
     output:
-        "Samplesize/GISTIC/Size{rand_nr}.Rep{rep_nr}/all_lesions.conf_" + config["gistic_precision"] + ".txt"
+        "Samplesize/GISTIC/Size{rand_nr}.Rep{rep_nr}/all_lesions.conf_" + config["gistic_precision"] + ".txt",
         "Samplesize/GISTIC/Size{rand_nr}.Rep{rep_nr}/regions_track.conf_" + config["gistic_precision"] + ".bed"
     params:
         cnv="",

run_pipeline_cluster.sh

@@ -18,8 +18,8 @@ snakemake -p \
 	--configfile config.yaml \
 	--snakefile Snakefile \
 	--latency-wait 90 \
-	--jobs 3 \
+	--jobs 1 \
 	--max-jobs-per-second 10 \
-	--restart-times 3 \
-	--use-conda \
-	--conda-prefix ~/.conda
+	--restart-times 3 
+#	--use-conda \
+#	--conda-prefix ~/.conda

wrappers/GISTIC2/environment.yaml

 channels:
     - bioconda
-    - conda-forge