From fad1aca5005b69046ab5a2a570bdbaf168dbcaec Mon Sep 17 00:00:00 2001 From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu> Date: Sun, 8 Jul 2018 22:08:22 -0500 Subject: [PATCH] Remove depreciated bash scripts --- bash.scripts/sc_CIAnalysis-Pr.sh | 26 ------------------------ bash.scripts/sc_FullAnalysis-D17PrF.sh | 25 ----------------------- bash.scripts/sc_FullAnalysis-D27PrF.sh | 25 ----------------------- bash.scripts/sc_FullAnalysis-DPrF.sh | 28 -------------------------- bash.scripts/sc_FullAnalysis.sh | 25 ----------------------- 5 files changed, 129 deletions(-) delete mode 100644 bash.scripts/sc_CIAnalysis-Pr.sh delete mode 100755 bash.scripts/sc_FullAnalysis-D17PrF.sh delete mode 100755 bash.scripts/sc_FullAnalysis-D27PrF.sh delete mode 100644 bash.scripts/sc_FullAnalysis-DPrF.sh delete mode 100755 bash.scripts/sc_FullAnalysis.sh diff --git a/bash.scripts/sc_CIAnalysis-Pr.sh b/bash.scripts/sc_CIAnalysis-Pr.sh deleted file mode 100644 index 79d279a..0000000 --- a/bash.scripts/sc_CIAnalysis-Pr.sh +++ /dev/null @@ -1,26 +0,0 @@ -#!/bin/bash -#SBATCH --job-name R_CIAnalysis -#SBATCH -p super -#SBATCH -N 1 -#SBATCH -t 0-1:0:0 -#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_Demultiplex.R -Rscript ../r.scritps/sc_D-SampleReorder.R -Rscript ../r.scripts/sc_Seurat.Score.CellCycle.R -Rscript ../r.scripts/sc_QC.R -Rscript ../r.scripts/sc_Cluster.R -Rscript ../r.scripts/sc_PC.Score.Stress.R --sv=NA -Rscript ../r.scripts/sc_QuSAGE.Lineage.R --s=NA -Rscript ../r.scripts/sc_LineageSubClust.R -Rscript ../r.scripts/sc_QuSAGE_EpiSubClust.R --s=NA --r=0.2 -Rscript ../r.scripts/sc_QuSAGE_StSubClust.R --s=NA --r=0.2 -Rscript ../r.scripts/sc_MergeSubClust.R --r=0.2 -Rscript ../r.scripts/sc_PC.Score.NE.R --sv=NA -Rscript ../r.scripts/sc_DEG.R -Rscript ../r.scripts/sc_Tables.R diff --git a/bash.scripts/sc_FullAnalysis-D17PrF.sh b/bash.scripts/sc_FullAnalysis-D17PrF.sh deleted file mode 100755 index 8200e96..0000000 --- a/bash.scripts/sc_FullAnalysis-D17PrF.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash -#SBATCH --job-name R_FullAnalysis -#SBATCH -p 128GB,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_Demultiplex.R --p="D17PrF" --d=3 -Rscript ../r.scripts/sc_Seurat.Score.CellCycle.R --p="D17PrF" -Rscript ../r.scripts/sc_QC.R --p="D17PrF" -Rscript ../r.scripts/sc_Cluster.R --p="D17PrF" --pc=0 -Rscript ../r.scripts/sc_PC.Score.Stress.R --p="D17PrF" --r=0.5 --pc=0 -Rscript ../r.scripts/sc_QuSAGE.Lineage.R --p="D17PrF" --r=0.1 --s=NA -Rscript ../r.scripts/sc_LineageSubClust.R --p="D17PrF" --pc=0 -Rscript ../r.scripts/sc_QuSAGE_EpiSubClust.R --p="D17PrF" --r=0.1 --s=NA -Rscript ../r.scripts/sc_QuSAGE_StSubClust.R --p="D17PrF" --r=0.1 --s=NA -Rscript ../r.scripts/sc_MergeSubClust.R --p="D17PrF" -Rscript ../r.scripts/sc_PC.Score.NE.R --p="D17PrF" -Rscript ../r.scripts/sc_DEG.R --p="D17PrF" -Rscript ../r.scripts/sc_Tables.R --p="D17PrF" diff --git a/bash.scripts/sc_FullAnalysis-D27PrF.sh b/bash.scripts/sc_FullAnalysis-D27PrF.sh deleted file mode 100755 index 3471438..0000000 --- a/bash.scripts/sc_FullAnalysis-D27PrF.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/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_Demultiplex.R --p="D27PrF" --d=3 -Rscript ../r.scripts/sc_Seurat.Score.CellCycle.R --p="D27PrF" -Rscript ../r.scripts/sc_QC.R --p="D27PrF" -Rscript ../r.scripts/sc_Cluster.R --p="D27PrF" --pc=0 -Rscript ../r.scripts/sc_PC.Score.Stress.R --p="D27PrF" --r=0.5 --pc=0 --u=TRUE -Rscript ../r.scripts/sc_QuSAGE.Lineage.R --p="D27PrF" --gs="sc" --r=0.1 --s=NA -Rscript ../r.scripts/sc_LineageSubClust.R --p="D27PrF" --pc=0 -Rscript ../r.scripts/sc_QuSAGE_EpiSubClust.R --p="D27PrF" --r=0.2 --s=NA --sc=TRUE -Rscript ../r.scripts/sc_QuSAGE_StSubClust.R --p="D27PrF" --r=0.2 --s=NA --sc=TRUE -Rscript ../r.scripts/sc_MergeSubClust.R --p="D27PrF" --e="sc" --s="sc" -Rscript ../r.scripts/sc_PC.Score.NE.R --p="D27PrF" --u=TRUE -Rscript ../r.scripts/sc_DEG.R --p="D27PrF" -Rscript ../r.scripts/sc_Tables.R --p="D27PrF" diff --git a/bash.scripts/sc_FullAnalysis-DPrF.sh b/bash.scripts/sc_FullAnalysis-DPrF.sh deleted file mode 100644 index 49f9553..0000000 --- a/bash.scripts/sc_FullAnalysis-DPrF.sh +++ /dev/null @@ -1,28 +0,0 @@ -#!/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_Demultiplex.R --p="DPrF" --d=3 -#Rscript ../r.scripts/sc_Seurat.Score.CellCycle.R --p="DPrF" -#Rscript ../r.scripts/sc_QC.R --p="DPrF" - -Rscript ../r.scripts/sc_DIY.DPrF.aggr.R - -Rscript ../r.scripts/sc_Cluster.R --p="DPrF" --pc=0 -Rscript ../r.scripts/sc_PC.Score.Stress.R --p="DPrF" --r=1 --pc=0 --u=TRUE -Rscript ../r.scripts/sc_QuSAGE.Lineage.R --p="DPrF" --gs="sc" --r=0.5 --s=NA -Rscript ../r.scripts/sc_LineageSubClust.R --p="DPrF" --pc=0 -Rscript ../r.scripts/sc_QuSAGE_EpiSubClust.R --p="DPrF" --r=1 --s=NA --sc=TRUE -Rscript ../r.scripts/sc_QuSAGE_StSubClust.R --p="DPrF" --r=1 --s=NA --sc=TRUE -Rscript ../r.scripts/sc_MergeSubClust.R --p="DPrF" --e="sc" --s="sc" -Rscript ../r.scripts/sc_PC.Score.NE.R --p="DPrF" --u=TRUE -#Rscript ../r.scripts/sc_DEG.R --p="DPrF" -Rscript ../r.scripts/sc_Tables.R --p="DPrF" diff --git a/bash.scripts/sc_FullAnalysis.sh b/bash.scripts/sc_FullAnalysis.sh deleted file mode 100755 index 19f4d03..0000000 --- a/bash.scripts/sc_FullAnalysis.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash -#SBATCH --job-name R_FullAnalysis -#SBATCH -p 128B,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_Demultiplex.R -Rscript ../r.scripts/sc_Seurat.Score.CellCycle.R -Rscript ../r.scripts/sc_QC.R -Rscript ../r.scripts/sc_Cluster.R -Rscript ../r.scripts/sc_PC.Score.Stress.R -Rscript ../r.scripts/sc_QuSAGE.Lineage.R -Rscript ../r.scripts/sc_LineageSubClust.R -Rscript ../r.scripts/sc_QuSAGE_EpiSubClust.R -Rscript ../r.scripts/sc_QuSAGE_StSubClust.R -Rscript ../r.scripts/sc_MergeSubClust.R -Rscript ../r.scripts/sc_PC.Score.NE.R -Rscript ../r.scripts/sc_DEG.R -Rscript ../r.scripts/sc_Tables.R -- GitLab