Removed scripts which are not used.

config_laptop.yaml

-#Directories to be specified
-#workdir: /home/bftan/CNA_results        #directory to write output
-#gisticdir: /home/bftan/Tools/GISTIC2_test    #directory to install GISTIC2
-
-#workdir: /home/bftan/CNA_results        #directory to write output
-#gisticdir: /home/bftan/Tools/GISTIC2    #directory to install GISTIC2
-
-workdir: /home/beatrice/CNA_analysis
-gisticdir: /home/beatrice/CNA_analysis/run_gistic2
-
-#Input details to download from firehose
-cancer_type: SKCM
-date_data: "2016_07_15"
-
-#Or provide input file
-inputfile: ""   #tumor segmentation data
-normal: ""      #normal segmentation data
-
-#Data for running and benchmarking tools.
-reference: hg19
-prev_found_genes: input_files/intogen-CM-drivers-data.tsv
-census_genes: input_files/Census_genes.txt
-biomart_genes: input_files/biomart_human_genes.tsv
-
-#Settings GISTIC2.0
-gistic_precision: "99"
-settings_gistic: "-ta 0.1
-                  -td 0.1
-                  -qvt 0.25
-                  -brlen 0.7
-                  -cap 1.5
-                  -rx 1
-                  -genegistic 1
-                  -conf 0.99"
-
-#Settings for sample size differences
-sizes: [20, 30, 40, 50, 60, 70, 80, 90]
-#sizes: [30, 40]
-repeats: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]

scripts/plot_regions.R

-#!/usr/bin/env Rscript
-args = commandArgs(trailingOnly=TRUE)
-
-source("https://bioconductor.org/biocLite.R")
-biocLite("karyoploteR")
-
-bed = read.table(args[1], sep="\t", header=TRUE)
-#Read output plot files?
-#chrom as "chr1"
-kp <- plotKaryotype(chromosomes=c(chrom))
-#kpDataBackground(kp)
-kpAxis(kp)
-kpRect(kp, chr=chrom, x0=start, x1=end, y0=0.2, y1=0.4)