Tools‎ > ‎Ubuntu/Linux server‎ > ‎

gzip & tar.gz

Decompression

.zip

# decompress .zip  folder (as used in Windows)
unzip samples.zip

.gz

# decompress .gz file (compressed .gz file will be removed after decompression)
gzip -d sample.fastq.gz
  sample.fastq

# view the content of a .gz file
zcat sample.fastq.gz

 # view top 20 line  - pass decompressed content via unix pipe to head command
zcat sample.fastq.gz | head -20 

.tar.gz

# tar   decompress .tar.gz files
tar -zxvf samples.tar.gz

# unix pipe  pass decompressed file into a pipe: extract all tar archive files to standard output (option -O)
tar -zxOf samples.tar.gz | head -20   # views the first 20 lines


Compression

# compress single file gzip (original file will be removed after compression)
gzip sample.fastq
 sample.fastq.gz


# compress complete directory
# tar archive (tar.gz is recommended standard in Linux)
tar -zcvf samples_compressed.tar.gz /path/to/sample/directory/

# compress a complete folder as single zip file for using in Windows (not gzip)
zip -r samples.zip sample_folder/


# to change gzip level used in tar archive (default compression level is 6, max level is 9)
# a) providing the compression command by option -I
tar -I 'gzip -9' -cvf samples_compressed.tar.gz sample_directory/
# b) combine tar and gzip using a unix pipe
tar cvf - sample_directory/  | gzip -9 > samples_compressed.tar.gz



Extract single file from tar archive


# list content (all files) of a .tar.gz archive
tar -tf samples.tar.gz
sample_1.fastq
sample_2.fastq

# extract selected file from .tar.gz archive
tar -zxvf samples.tar.gz sample_1.fastq
sample_1.fastq




# install zip and unzip
sudo apt install zip unzip