Develop

bash.scripts/sc10x.RUN.sh

+#!/bin/bash
+#SBATCH --job-name sc10x.dispatch
+#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
+
+git pull origin Seurat3.0
+rm ../analysis/*.rda
+rm ../analysis/*.RData
+rm -r ../analysis/cor/
+rm -r ../analysis/qc/
+rm -r ../analysis/score_id/
+rm -r ../analysis/shiny/
+rm -r ../analysis/vis/
+
+module load python/3.6.4-anaconda 
+source activate umap
+module load R/3.5.1-gccmkl
+module load hdf5_18/1.8.17
+Rscript ../r.scripts/sc-TissueMapper_RUN.R --p "$1" --s "$2"
+
+module unload R/3.5.1-gccmkl
+module load R/3.6.1-gccmkl
+if [[ "$1" == "PdPgb" ]] || [[ "$1" == "PdPb" ]]
+then
+	Rscript ../r.scripts/SingleR.R --p "$1" --s "$2" --o "$3"
+elif [[ "$3" == "epi" ]] || [["$3" == "fmst" ]]
+then
+	Rscript ../r.scripts/huPr_muPr.R --p "$1" --r "$3"
+fi
+
+module unload R/3.5.1-gccmkl
+module load R/3.6.1-gccmkl
+if [[ "$1" == "PdPgb" ]]
+then
+	Rscript ../r.scripts/diy_PdPgb.R
+elif [[ "$3" == "epi" ]]
+then
+	Rscript ../r.scripts/diy_muPrUr_Epi.R
+fi