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Commit fad1aca5 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Remove depreciated bash scripts

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bash.scripts/sc_CIAnalysis-Pr.sh deleted 100644 → 0
+ 0
− 26
View file @ afa97489
#!/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
bash.scripts/sc_FullAnalysis-D17PrF.sh deleted 100755 → 0
+ 0
− 25
View file @ afa97489
#!/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"
bash.scripts/sc_FullAnalysis-D27PrF.sh deleted 100755 → 0
+ 0
− 25
View file @ afa97489
#!/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"
bash.scripts/sc_FullAnalysis-DPrF.sh deleted 100644 → 0
+ 0
− 28
View file @ afa97489
#!/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"
bash.scripts/sc_FullAnalysis.sh deleted 100755 → 0
+ 0
− 25
View file @ afa97489
#!/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
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