From 2673f2f86d59165e1fb0f4c31e3bd7d9a74b51e0 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 18 Jun 2018 08:01:33 -0500
Subject: [PATCH] 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 | 13 +++++++++++++
bash.scripts/sc_TissueMapper-DPrF.sh | 13 +++++++++++++
r.scripts/sc-TissueMapper_RUN.D.R | 2 +-
r.scripts/sc-TissueMapper_RUN.D17.R | 2 +-
r.scripts/sc-TissueMapper_RUN.D27.R | 2 +-
5 files changed, 29 insertions(+), 3 deletions(-)
create mode 100644 bash.scripts/sc_TissueMapper-D17PrF.sh
create mode 100644 bash.scripts/sc_TissueMapper-DPrF.sh
diff --git a/bash.scripts/sc_TissueMapper-D17PrF.sh b/bash.scripts/sc_TissueMapper-D17PrF.sh
new file mode 100644
index 0000000..af8272b
--- /dev/null
+++ b/bash.scripts/sc_TissueMapper-D17PrF.sh
@@ -0,0 +1,13 @@
+#!/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
diff --git a/bash.scripts/sc_TissueMapper-DPrF.sh b/bash.scripts/sc_TissueMapper-DPrF.sh
new file mode 100644
index 0000000..c38f8a9
--- /dev/null
+++ b/bash.scripts/sc_TissueMapper-DPrF.sh
@@ -0,0 +1,13 @@
+#!/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
diff --git a/r.scripts/sc-TissueMapper_RUN.D.R b/r.scripts/sc-TissueMapper_RUN.D.R
index 8c6c44b..5212d74 100644
--- a/r.scripts/sc-TissueMapper_RUN.D.R
+++ b/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("../")
diff --git a/r.scripts/sc-TissueMapper_RUN.D17.R b/r.scripts/sc-TissueMapper_RUN.D17.R
index 8dce59e..eca50e4 100644
--- a/r.scripts/sc-TissueMapper_RUN.D17.R
+++ b/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("../")
diff --git a/r.scripts/sc-TissueMapper_RUN.D27.R b/r.scripts/sc-TissueMapper_RUN.D27.R
index 6f4b068..89fa46e 100644
--- a/r.scripts/sc-TissueMapper_RUN.D27.R
+++ b/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("../")
--
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