Skip to content

Latest commit

 

History

History
138 lines (123 loc) · 2.59 KB

linux.md

File metadata and controls

138 lines (123 loc) · 2.59 KB
Raw

Change permissions

change all document in this file

chmod /fs/project/PAS1475/guoqi/spatial_data/ -R 777
chmod -R 777 *
Note: do not use blank when name folder

compress and decompress file

compress

gzip FileName

decompress file

end with zip

unzip FileName.zip

end with gz--gzip

gzip -d FileName.gz

end with tar.gz-tar

tar zxvf FileName.tar.gz

Copy file

cd originalpath
cp file targetpath

R

start R in terminal

module load R/4.1.0-gnu9.1
R

quit R in terminal

quit()

load JOB on server

#upload
sbatch xxx.sh
#supervise
qstat jobname
qstat -u guoqi
https://maveric-informatics.readthedocs.io/en/latest/OSC.html

transfer file by remote server

scp -r guoqi@192.148.247.179:/fs/ess/PCON0022/guoqi/NC-snrna/atac_output/temp ./rawdata/temp

Run sh script

/bin/bash .command.sh

Find specific file

specific file in this path
cd path
find ./ -iname projection*
#find specific file in all path
find . -type f -name "*h5Seurat*"

Check object storage

du -ah

Show all files including hidden

ls -a

OSC

create sh command

#!/bin/bash
#SBATCH --job-name=directnet_examp
#SBATCH --time=20:50:59
#SBATCH --output="directnet_sh_out"
#SBATCH --account=PCON0022
#SBATCH --mem=150GB
#SBATCH --mail-type=BEGIN,END,FAIL

cd /fs/ess/PCON0022/guoqi/Yang/Stream/Directnet
start=`date +%s`
module load R/4.1.0-gnu9.1
Rscript /fs/ess/PCON0022/guoqi/Yang/Stream/Directnet/Directnet.r
end=`date +%s`
echo Execution time was `expr $end - $start` seconds.

Change file name in batch

for file in *_expression*; do     mv -- "$file" "${file//_expression}"; done
for file in sim_*; do     new_name=$(echo "$file" | sed 's/_/-/g');     mv "$file" "$new_name"; done
for file in *.h5ad*; do
    newname="${file/.h5ad/_sim_sim_expression.h5ad}"
    mv -- "$file" "$newname"
done
for file in *.h5Seurat*; do
    newname="${file/.h5Seurat/_sim_sim_expression.h5Seurat}"
    mv -- "$file" "$newname"
done

for file in *_xy*; do     mv -- "$file" "${file//_xy}"; done
for file in sim_*; do     new_name=$(echo "$file" | sed 's/_/-/g');     mv "$file" "$new_name"; done
for file in *.csv*; do
    newname="${file/.csv/_sim_sim_xy.csv}"
    mv -- "$file" "$newname"
done

Submit jobs on VP3

Submit

conda activate virtualenvironment
nohup python ./05_Subcluster_integration_evaluate.py > output_05.txt 2>&1 &

Check jobs

jobs

Check id and cancel

ps aux | grep 04_Integration_scvi.py
#id is the first number in the first row : 633763
kill id