From 295a0dcf199a9e8ec13d608d071d317b848ef0ed Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 12 Feb 2018 14:44:13 -0600
Subject: [PATCH] Update bash.scripts and r.scripts to use R 3.4.1
---
bash.scripts/sc_FullAnalysis-Pr.sh | 2 +-
r.scripts/sc_Cluster.R | 2 +-
r.scripts/sc_D-SampleReorder.R | 2 +-
r.scripts/sc_DEG.R | 2 +-
r.scripts/sc_Demultiplex.R | 2 +-
r.scripts/sc_PC.Score.NE.R | 2 +-
r.scripts/sc_PC.Score.Stress.R | 2 +-
r.scripts/sc_QC.R | 2 +-
r.scripts/sc_QuSAGE.Epi.R | 2 +-
r.scripts/sc_QuSAGE.LGEA.Epi.R | 2 +-
r.scripts/sc_QuSAGE.LGEA.St.R | 2 +-
r.scripts/sc_QuSAGE.Lineage.R | 2 +-
r.scripts/sc_QuSAGE.St.R | 2 +-
r.scripts/sc_Seurat.Score.CellCycle.R | 2 +-
r.scripts/sc_Tables.R | 2 +-
r.scripts/sc_mkGSEA.R | 2 +-
16 files changed, 16 insertions(+), 16 deletions(-)
diff --git a/bash.scripts/sc_FullAnalysis-Pr.sh b/bash.scripts/sc_FullAnalysis-Pr.sh
index abfa320..b74b0ca 100755
--- a/bash.scripts/sc_FullAnalysis-Pr.sh
+++ b/bash.scripts/sc_FullAnalysis-Pr.sh
@@ -30,7 +30,7 @@
#SBATCH --mail-type ALL
#SBATCH --mail-user gervaise.henry@utsouthwestern.edu
-module load R/3.3.2-gccmkl
+module load R/3.4.1-gccmkl
# COMMAND GROUP 1
Rscript ../r.scripts/sc_Demultiplex.R
diff --git a/r.scripts/sc_Cluster.R b/r.scripts/sc_Cluster.R
index b5d2ff8..3eb76eb 100755
--- a/r.scripts/sc_Cluster.R
+++ b/r.scripts/sc_Cluster.R
@@ -1,5 +1,5 @@
gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
library(optparse)
library(Seurat)
library(readr)
diff --git a/r.scripts/sc_D-SampleReorder.R b/r.scripts/sc_D-SampleReorder.R
index 6d4ed1a..bbc6850 100755
--- a/r.scripts/sc_D-SampleReorder.R
+++ b/r.scripts/sc_D-SampleReorder.R
@@ -1,5 +1,5 @@
gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
library(optparse)
library(Seurat)
diff --git a/r.scripts/sc_DEG.R b/r.scripts/sc_DEG.R
index 9333b15..7094ff7 100755
--- a/r.scripts/sc_DEG.R
+++ b/r.scripts/sc_DEG.R
@@ -1,5 +1,5 @@
gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
library(optparse)
library(Seurat)
diff --git a/r.scripts/sc_Demultiplex.R b/r.scripts/sc_Demultiplex.R
index c9dfcb4..593aca6 100755
--- a/r.scripts/sc_Demultiplex.R
+++ b/r.scripts/sc_Demultiplex.R
@@ -1,5 +1,5 @@
gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
library(optparse)
library(Seurat)
library(readr)
diff --git a/r.scripts/sc_PC.Score.NE.R b/r.scripts/sc_PC.Score.NE.R
index 2176e1d..de94acb 100755
--- a/r.scripts/sc_PC.Score.NE.R
+++ b/r.scripts/sc_PC.Score.NE.R
@@ -1,5 +1,5 @@
gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
library(optparse)
library(Seurat)
library(readr)
diff --git a/r.scripts/sc_PC.Score.Stress.R b/r.scripts/sc_PC.Score.Stress.R
index 40629aa..0e2dae8 100755
--- a/r.scripts/sc_PC.Score.Stress.R
+++ b/r.scripts/sc_PC.Score.Stress.R
@@ -1,5 +1,5 @@
gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
library(optparse)
library(Seurat)
library(readr)
diff --git a/r.scripts/sc_QC.R b/r.scripts/sc_QC.R
index a7acbed..68689da 100755
--- a/r.scripts/sc_QC.R
+++ b/r.scripts/sc_QC.R
@@ -1,5 +1,5 @@
gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
library(optparse)
library(Seurat)
library(readr)
diff --git a/r.scripts/sc_QuSAGE.Epi.R b/r.scripts/sc_QuSAGE.Epi.R
index d93b26b..a0270fb 100755
--- a/r.scripts/sc_QuSAGE.Epi.R
+++ b/r.scripts/sc_QuSAGE.Epi.R
@@ -1,5 +1,5 @@
gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
library(optparse)
library(Seurat)
library(readr)
diff --git a/r.scripts/sc_QuSAGE.LGEA.Epi.R b/r.scripts/sc_QuSAGE.LGEA.Epi.R
index dc595a8..5d0660f 100755
--- a/r.scripts/sc_QuSAGE.LGEA.Epi.R
+++ b/r.scripts/sc_QuSAGE.LGEA.Epi.R
@@ -1,5 +1,5 @@
gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
library(optparse)
library(Seurat)
library(readr)
diff --git a/r.scripts/sc_QuSAGE.LGEA.St.R b/r.scripts/sc_QuSAGE.LGEA.St.R
index f684d6a..615f53b 100755
--- a/r.scripts/sc_QuSAGE.LGEA.St.R
+++ b/r.scripts/sc_QuSAGE.LGEA.St.R
@@ -1,5 +1,5 @@
gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
library(optparse)
library(Seurat)
library(readr)
diff --git a/r.scripts/sc_QuSAGE.Lineage.R b/r.scripts/sc_QuSAGE.Lineage.R
index 5bcb1cb..3ef0770 100755
--- a/r.scripts/sc_QuSAGE.Lineage.R
+++ b/r.scripts/sc_QuSAGE.Lineage.R
@@ -1,5 +1,5 @@
gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
library(optparse)
library(Seurat)
library(readr)
diff --git a/r.scripts/sc_QuSAGE.St.R b/r.scripts/sc_QuSAGE.St.R
index 6932444..8377620 100755
--- a/r.scripts/sc_QuSAGE.St.R
+++ b/r.scripts/sc_QuSAGE.St.R
@@ -1,4 +1,4 @@
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
library(optparse)
library(Seurat)
library(readr)
diff --git a/r.scripts/sc_Seurat.Score.CellCycle.R b/r.scripts/sc_Seurat.Score.CellCycle.R
index 628e30f..d1d0676 100755
--- a/r.scripts/sc_Seurat.Score.CellCycle.R
+++ b/r.scripts/sc_Seurat.Score.CellCycle.R
@@ -1,5 +1,5 @@
gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
library(optparse)
library(Seurat)
library(readr)
diff --git a/r.scripts/sc_Tables.R b/r.scripts/sc_Tables.R
index 0267229..0964814 100755
--- a/r.scripts/sc_Tables.R
+++ b/r.scripts/sc_Tables.R
@@ -1,5 +1,5 @@
gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
library(optparse)
library(Seurat)
diff --git a/r.scripts/sc_mkGSEA.R b/r.scripts/sc_mkGSEA.R
index 761e876..6952e4e 100755
--- a/r.scripts/sc_mkGSEA.R
+++ b/r.scripts/sc_mkGSEA.R
@@ -1,4 +1,4 @@
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
library(optparse)
library(Seurat)
library(readr)
--
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