Refactor

bash.scripts/sc10x.RUN.sh

@@ -8,37 +8,9 @@
 #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 gdal
+module load cairo/1.14.8
+module load R/4.0.2-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" == "huPr_PdPgb" ]] || [[ "$1" == "huPr_PdPb" ]] || [[ "$1" == "huBl" ]]
-then
-	Rscript ../r.scripts/SingleR.R --p "$1" --s "$2" --o "$3"
-elif [[ "$1" == "muPrUr" ]]
-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" == "huPr_PdPgb" ]]
-then
-	Rscript ../r.scripts/diy_PdPgb.R
-elif [[ "$1" == "muPrUr" ]]
-then
-	Rscript ../r.scripts/diy_muPrUr_Epi.R
-fi
+Rscript ../r.scripts/sc-TissueMapper_RAW.R --p "$1" --s "$2" --m "$3"
+Rscript ../r.scripts/sc-TissueMapper_ID.R --p "$1" --s "$2" --o "$4"