Commit 6402104a authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Add project name opt and bash script for raw (initial) analysis

parent 35d35581
#!/bin/bash
#SBATCH --job-name sc10x.raw
#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 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
......@@ -18,12 +18,19 @@ library(autothresholdr)
options(bitmapType="cairo")
option_list=list(
make_option("--p",action="store",default="data",type='character',help="Project Name")
)
opt=parse_args(OptionParser(option_list=option_list))
rm(option_list)
setwd("../")
source("./r.scripts/sc-TissueMapper_functions.R")
source("./r.scripts/sc-TissueMapper_process.R")
project.name="Biopsy"
project.name=opt$p
scFolders()
......
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