From 04269b42ac2f363f4a638ac6965e049546fb005e Mon Sep 17 00:00:00 2001 From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu> Date: Thu, 19 Apr 2018 12:14:19 -0500 Subject: [PATCH] Add 128GB and 384GB partitions as option for FullAnalysis bash scripts, also clean up all bash scripts --- bash.scripts/sc_CIAnalysis-Pr.sh | 30 +++--------------------------- bash.scripts/sc_FullAnalysis-Pr.sh | 28 ++-------------------------- 2 files changed, 5 insertions(+), 53 deletions(-) diff --git a/bash.scripts/sc_CIAnalysis-Pr.sh b/bash.scripts/sc_CIAnalysis-Pr.sh index 6decace..f402960 100644 --- a/bash.scripts/sc_CIAnalysis-Pr.sh +++ b/bash.scripts/sc_CIAnalysis-Pr.sh @@ -1,38 +1,15 @@ #!/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_CIAnalysis - -# Name of the SLURM partition that this job should run on. -#SBATCH -p super # partition (queue) -# Number of nodes required to run this job +#SBATCH -p super #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 -t 0-1:0:0 #SBATCH -o job_%j.out -#SBATCH -e job_%j.err - -# Send an email when the job status changes, to the specfied address. +#SBATCH -e job_%j.out #SBATCH --mail-type ALL #SBATCH --mail-user gervaise.henry@utsouthwestern.edu module load R/3.3.2-gccmkl -# COMMAND GROUP 1 Rscript ../r.scripts/sc_Demultiplex.R Rscript ../r.scritps/sc_D-SampleReorder.R Rscript ../r.scripts/sc_Seurat.Score.CellCycle.R @@ -47,4 +24,3 @@ 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 -# END OF SCRIPT diff --git a/bash.scripts/sc_FullAnalysis-Pr.sh b/bash.scripts/sc_FullAnalysis-Pr.sh index f830bf0..a610938 100755 --- a/bash.scripts/sc_FullAnalysis-Pr.sh +++ b/bash.scripts/sc_FullAnalysis-Pr.sh @@ -1,38 +1,15 @@ #!/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 -p 128B,256GB,256GBv1,384GB #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 -e job_%j.out #SBATCH --mail-type ALL #SBATCH --mail-user gervaise.henry@utsouthwestern.edu module load R/3.3.2-gccmkl -# COMMAND GROUP 1 Rscript ../r.scripts/sc_Demultiplex.R Rscript ../r.scritps/sc_D-SampleReorder.R Rscript ../r.scripts/sc_Seurat.Score.CellCycle.R @@ -47,4 +24,3 @@ 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 -# END OF SCRIPT -- GitLab