Add bash scripts for runnting TissueMapper and fix r.scripts to allow the...

Add bash scripts for runnting TissueMapper and fix r.scripts to allow the pipeline to run from bash script folder

bash.scripts/sc_TissueMapper-D17PrF.sh

+#!/bin/bash
+#SBATCH --job-name R_FullAnalysis
+#SBATCH -p 256GB,256GBv1,384GB
+#SBATCH -N 1
+#SBATCH -t 7-0:0:0
+#SBATCH -o job_%j.out
+#SBATCH -e job_%j.out
+#SBATCH --mail-type ALL
+#SBATCH --mail-user gervaise.henry@utsouthwestern.edu
+
+module load R/3.4.1-gccmkl
+
+Rscript ../r.scripts/sc-TissueMapper_RUN.D17.R
\ No newline at end of file

bash.scripts/sc_TissueMapper-DPrF.sh

+#!/bin/bash
+#SBATCH --job-name R_FullAnalysis
+#SBATCH -p 256GB,256GBv1,384GB
+#SBATCH -N 1
+#SBATCH -t 7-0:0:0
+#SBATCH -o job_%j.out
+#SBATCH -e job_%j.out
+#SBATCH --mail-type ALL
+#SBATCH --mail-user gervaise.henry@utsouthwestern.edu
+
+module load R/3.4.1-gccmkl
+
+Rscript ../r.scripts/sc-TissueMapper_RUN.D.R
\ No newline at end of file

r.scripts/sc-TissueMapper_RUN.D.R

@@ -7,7 +7,7 @@ library(fBasics)
 library(pastecs)
 library(qusage)
 
-source("sc-TissueMapper.R")
+source("../r.scripts/sc-TissueMapper.R")
 
 #Create folder structure
 setwd("../")

r.scripts/sc-TissueMapper_RUN.D17.R

@@ -7,7 +7,7 @@ library(fBasics)
 library(pastecs)
 library(qusage)
 
-source("sc-TissueMapper.R")
+source("../r.scripts/sc-TissueMapper.R")
 
 #Create folder structure
 setwd("../")

r.scripts/sc-TissueMapper_RUN.D27.R

@@ -7,7 +7,7 @@ library(fBasics)
 library(pastecs)
 library(qusage)
 
-source("sc-TissueMapper.R")
+source("../r.scripts/sc-TissueMapper.R")
 
 #Create folder structure
 setwd("../")