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Commit 21f4f870 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Update FullAnalyis sh from Pr to D17PrF

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bash.scripts/sc_FullAnalysis-D17PrF.sh 0 → 100755
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#!/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 --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"
Rscript ../r.scripts/sc_PC.Score.Stress.R --p="D17PrF"
Rscript ../r.scripts/sc_QuSAGE.Lineage.R --p="D17PrF"
Rscript ../r.scripts/sc_LineageSubClust.R --p="D17PrF"
Rscript ../r.scripts/sc_QuSAGE_EpiSubClust.R --p="D17PrF"
Rscript ../r.scripts/sc_QuSAGE_StSubClust.R --p="D17PrF"
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-DPrF-Lin.sh deleted 100644 → 0
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− 37
View file @ 1caf21f6
#!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Thu Nov 30 2017 16:16:26 GMT-0600 (Central Standard Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# Lines starting with #SBATCH specify options for the scheduler.
# Lines that do not start with # or #SBATCH are commands that will run.
# Name for the job that will be visible in the job queue and accounting tools.
#SBATCH --job-name R_FullAnalysis
# Name of the SLURM partition that this job should run on.
#SBATCH -p 256GB,256GBv1 # partition (queue)
# Number of nodes required to run this job
#SBATCH -N 1
# Time limit for the job in the format Days-H:M:S
# A job that reaches its time limit will be cancelled.
# Specify an accurate time limit for efficient scheduling so your job runs promptly.
#SBATCH -t 7-0:0:0
# The standard output and errors from commands will be written to these files.
# %j in the filename will be replace with the job number when it is submitted.
#SBATCH -o job_%j.out
#SBATCH -e job_%j.err
# Send an email when the job status changes, to the specfied address.
#SBATCH --mail-type ALL
#SBATCH --mail-user gervaise.henry@utsouthwestern.edu
module load R/3.4.1-gccmkl
# COMMAND GROUP 1
Rscript ../r.scripts/sc_QuSAGE.Lineage.R --p="DPrF"
# END OF SCRIPT
bash.scripts/sc_FullAnalysis-DPrF.sh deleted 100755 → 0
+ 0
− 50
View file @ 1caf21f6
#!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Thu Nov 30 2017 16:16:26 GMT-0600 (Central Standard Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# Lines starting with #SBATCH specify options for the scheduler.
# Lines that do not start with # or #SBATCH are commands that will run.
# Name for the job that will be visible in the job queue and accounting tools.
#SBATCH --job-name R_FullAnalysis
# Name of the SLURM partition that this job should run on.
#SBATCH -p 256GB,256GBv1 # partition (queue)
# Number of nodes required to run this job
#SBATCH -N 1
# Time limit for the job in the format Days-H:M:S
# A job that reaches its time limit will be cancelled.
# Specify an accurate time limit for efficient scheduling so your job runs promptly.
#SBATCH -t 7-0:0:0
# The standard output and errors from commands will be written to these files.
# %j in the filename will be replace with the job number when it is submitted.
#SBATCH -o job_%j.out
#SBATCH -e job_%j.err
# Send an email when the job status changes, to the specfied address.
#SBATCH --mail-type ALL
#SBATCH --mail-user gervaise.henry@utsouthwestern.edu
module load R/3.4.1-gccmkl
# COMMAND GROUP 1
Rscript ../r.scripts/sc_Demultiplex.R --p="DPrF" --d=7
#Rscript ../r.scritps/sc_D-SampleReorder.R
#Rscript ../r.scripts/sc_Seurat.Score.CellCycle.R --p="DPrF"
Rscript ../r.scripts/sc_QC.R --p="DPrF" --cc=FALSE
Rscript ../r.scripts/sc_Cluster.R --p="DPrF"
Rscript ../r.scripts/sc_PC.Score.Stress.R --p="DPrF"
#Rscript ../r.scripts/sc_QuSAGE.Lineage.R --p="DPrF"
#Rscript ../r.scripts/sc_LineageSubClust.R --p="DPrF"
#Rscript ../r.scripts/sc_QuSAGE_EpiSubClust.R --p="DPrF"
#Rscript ../r.scripts/sc_QuSAGE_StSubClust.R --p="DPrF"
#Rscript ../r.scripts/sc_MergeSubClust.R --p="DPrF"
#Rscript ../r.scripts/sc_PC.Score.NE.R --p="DPrF"
#Rscript ../r.scripts/sc_DEG.R --p="DPrF"
#Rscript ../r.scripts/sc_Tables.R --p="DPrF"
# END OF SCRIPT
bash.scripts/sc_FullAnalysis-Pr.sh deleted 100755 → 0
+ 0
− 26
View file @ 1caf21f6
#!/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.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
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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