bash_useful_commands.md

Download file from URL

wget https://data.qiime2.org/distro/core/qiime2-2020.11-py36-linux-conda.yml

Compress directory

tar -zcf GSE63042_kaiju.tar.gz Kaiju_Summary/

Copy file from local to remote server

scp covid-19.fasta  csbl-server:/home/CSBL/icaro/

Copy file from remote server to local

scp csbl-server:/home/CSBL/icaro/ncbi_error_report.xml report.xml

Copy entire folder from local to remote server

scp -r /home/icaro/covid_bali csbl-server:/home/CSBL/icaro/sandbox/

Copy entire folder from remote server to local

scp -r csbl-server:/home/CSBL/icaro/sandbox/metatranscriptomics/GSE152418/ /home/icaro/GSE152418

Move all files from subdirectories to current directory?

find . -type f -mindepth 2 -exec mv -i -- {} . \;

Clean up the whole bunch of empty subdirectories with

find . -depth -mindepth 1 -type d -empty -exec rmdir {} \;

Run command in background

Rscript 03_normalization_and_clustering.R & 

Run command in background and redirect output to a file nohup.out

nohup Rscript 03_normalization_and_clustering.R & 

Run command in background and redirect output to a file called 03_cite_seq.log

nohup Rscript 03_normalization_and_clustering.R &> 03_cite_seq.log & 

Download a list of files from HTTP/FTP Server

List top 5 directories occupying disk space

BONUS

Get number of mapped reads against reference

samtools view -F 0x904 -c covid-19_mapped.sam

Convert bam to fastq

samtools bam2fq SAMPLE.bam > SAMPLE.fastq

Replace spaces in filenames with underscores

for i in *' '*; do   mv "$i" `echo $i | sed -e 's/ /_/g'`; done