Update PopStratConfig.conf

update to v2.0.1

Author: Orion1618

SubModules/PopStratModule/PopStratConfig.conf

@@ -23,42 +23,31 @@
 
 # Specify the "Base" Name of your Reference Dataset (don't include extension -- .bed/.bim/.fam) (REQUIRED)
    # Note: The add-in will search for a BED/BIM/FAM file trio that has this name in the 'PLACE_Target-Ref_Datasets_HERE' directory within ./Odyssey/PopStratModule/
-	RefDataset="1000Genomes_Complete";
+	RefDataset="1000Genomes_GRCh37Mapped";
 
 
 # Specify the Name of your Target Dataset (don't include extension -- .bed/.bim/.fam) (REQUIRED)
    # Note: The add-in will search for a BED/BIM/FAM file trio that has this name in the 'PLACE_Target-Ref_Datasets_HERE' directory within ./Odyssey/PopStratModule/
-	TargetDataset="Plates1-48_Raw";
+	TargetDataset="Plates1-48_NoDups";
 
 
 # Specify a Name For the PCA Analysis (must not include any spaces) (REQUIRED)
    # The specified PCA analysis folder can be found within ./Odyssey/PCA_Analyses/
-	PCA_Analysis_Name="EyebrowsPCA";
+	PCA_Analysis_Name="PlotlyAddin";
 
 
 # To determine the number of principal components to keep the R analysis script looks at how much each Principal Component contributes to the total amount
    # of variance. Currently, principal components that contribute 1% or greater to total variance is kept. In turn the Principal Component's dimmension is 
    # used in the calculation of the N-dimmension reference centroid, which forms the basis on what individuals are kept/removed due to outlying ancestries (OPTIONAL)
-	PC_VariancePerc="0.01";
+	PC_VariancePerc="0.05";
 	PC_StandardDev="3";
 
 
 # Maximum Memory Allocation
    # Some Plink Commands (especially when handling larger datasets) try and allocate large amounts of memory
    # Specify the maximum memory allocation you can dedicate (this will be used to limit Plink's memory allocation and the amount of memory R will be allowed if executing on a HPS
    # Specify in terms of GB
-	Max_Memory="24";
-
-# ===========================================================================================================================================================================
-# ==================================================================== Program Dependencies =================================================================================
-# ===========================================================================================================================================================================
-
-# Specify Path to Plink Exec: (REQUIRED)
-	PlinkExec="/gpfs/home/r/y/ryeller/Carbonate/Programs/Plink_1.09/plink";
-
-# Set R Bin Directory: (REQUIRED for PCA Analysis/Visualization) -- see R installation instructions below for some tips to getting R and its package dependencies installed
-	# Put the path directory to the "bin" folder that contains your R.exe file
-		Rscript="/gpfs/home/r/y/ryeller/Carbonate/Programs/R/R-3.5.1/bin/Rscript";
+	Max_Memory="85";
 
 
 # ==================================================
@@ -89,24 +78,22 @@
 
 #----------------------------
 
+# ===========================================================================================================================================================================
+# ==================================================================== Program Dependencies =================================================================================
+# ===========================================================================================================================================================================
 
+# Specify Path to Plink Exec: (REQUIRED)
+	# Manual Setup 
+		#PlinkExec="/gpfs/home/r/y/ryeller/Carbonate/Programs/Plink_1.09/plink";
+	# Singularity Setup
+		PlinkExec="singularity exec ${WorkingDir}Configuration/Singularity/OdysseyContainer.sif plink ";
 
 
-# ====================================================
-#  R Installation Additional Help
-# ====================================================
-	# You will need to download and install the programming language R (plus some of its package dependencies) if you intend to use the visualization features of Odyssey
-	# To download a local installation of R in cases where you don't have admin privileges you should be able to execute the following command on terminal (remember to remove the #):
-		# NOTE: Change the --prefix file path to the directory you want R installed. This will cause R to be installed to a local directory (that you ideally have admin privaleges over)
-			# wget http://cran.rstudio.com/src/base/R-3/R-3.5.1.tar.gz; tar xvf R-3.5.1.tar.gz; cd R-3.5.1; ./configure --prefix=/gpfs/home/r/y/ryeller/Carbonate/Programs/R; make && make install
-	
-	# You will also need to install the R package dependencies: tidyverse, qqman, manhattanly, data.table
-		# You can do that by calling the R exec in terminal (R should then load) and then execute the following commented out lines
-		
-	#if(!require(tidyverse)) {install.packages('tidyverse', dependencies=T, repos='https://ftp.ussg.iu.edu/CRAN/', lib ='/gpfs/home/r/y/ryeller/Carbonate/Programs/R/R-3.5.1/library')}
-	#if(!require(data.table)) {install.packages('data.table', dependencies=T, repos='https://ftp.ussg.iu.edu/CRAN/', lib ='/gpfs/home/r/y/ryeller/Carbonate/Programs/R/R-3.5.1/library')}
-	#if(!require(ggplot2)) {install.packages('ggplot2', dependencies=T, repos='https://ftp.ussg.iu.edu/CRAN/', lib ='/gpfs/home/r/y/ryeller/Carbonate/Programs/R/R-3.5.1/library')}
-	#library(tidyverse, qqman, manhattanly, data.table)
+# Specify Path to Rscript directory: (REQUIRED)
+	# Manual Setup 	
+		#Rscript="/gpfs/home/r/y/ryeller/Carbonate/Programs/R/R-3.5.1/bin/Rscript";
+	# Singularity Setup
+		Rscript="singularity exec ${WorkingDir}Configuration/Singularity/OdysseyContainer.sif Rscript";