Shell Bash Slurm Command

So..., I find I used these codes a lot.

while IFS= read -r line; do
   python ./../PDB_ana.py ${line} /../test_clean/ 
done < <(grep "" ./pdb.txt)

ls -l | wc -l

wget -i links.txt -o wget.log

tar -tzf file.tar.gz | wc -l # count files in tar.gz without unzip # it actually counts lines, and it will cause counting \n as a line

tar -zcvf  myfolder.tar.gz myfolder

cp ./folder/*.txt ./newfolder

gunzip *.gz # for f in *.gz; do gunzip "$f"; done

cat *.fa > all_data.fa # concatenate multiple fasta files into one fasta file in command line

source ~/miniconda3/etc/profile.d/conda.sh
conda activate SE3nv

PDBdb_dir_has=()
for pdb_fp in $PDBdb_dir*pdb; do
    pdb=$(basename $pdb_fp .pdb)
    PDBdb_dir_has+=($pdb)
done

A=()
lines=`cat $AFDB_pLDDT_70_log`
for line in $lines; do
    if [[ $line  == *".pdb" ]]; then
        entry=$(echo "$line" | cut -d "." -f 1)
        A+=($entry)
    fi
done

How to discard changes in VScode?

Navigate to reporsitory (has .github folder) with changes. Then, git restore <file>

Activate conda environment in bash script

source ~/miniconda3/etc/profile.d/conda.sh
conda activate ENV

SBATCH Array jobs

#SBATCH -J array-job					
#SBATCH -a 1-3
#SBATCH -o array-job.%A.%a.log

id_list="./id_list.txt"
id=`head -n $SLURM_ARRAY_TASK_ID $id_list | tail -n 1`
python3 script.py -in $id

srun gpu

srun -N 1 --ntasks-per-node 2 -p v100 -q gpu --gres=gpu:1 --mem=50G --pty /bin/bash

run scripts

sbatch test.slm

check sequence process

squeue -u username

cancel sequence

scancel jobID

copy files into another folder

cp ./*.pdb ../newfoler

count files in a directory in command line

cd directory
ls -l | wc -l

# get .gz files
wget -r -np -e robots=off -A 'pep.all.fa.gz' https://ftp.ensembl.org/pub/current_fasta/

stat_gpu # check available  partition

srun -q gpu -p v100-af --mem=50G --gres=gpu:1 --pty /bin/bash # access one gpu

tar xvzf file.tar.gz # unzip

module load igv # access specific place

ls -1 | wc -l # count files in a directory in linux

Huilin's Book