Archive, compress and uncompress files

zip

zip is a compression and file packaging utility

• zip zipfile file1 file2 ...

  zip Nucleique.zip Nucleique/*
     adding: Nucleique/2Xseq.fasta (deflated 84%)
     adding: Nucleique/3_seq.fasta (deflated 57%)
     ...
  

exercice:

create a compress archive of all files in the Sequence/Proteique dir

unzip

unzip - list, test and extract compressed files in a ZIP archive

• unzip -l zipfile list archive files.
• unzip -t zipfile test archive files. This option extracts each specified file in memory and it's integrity.
• unzip zipfile
• unzip -d dir zipfile specify a directory to which to extract files.

exercice:

list, test and uncompress the zip archive proteique.zip that you did.

gzip

gzip compress files (does not make an archive!)

exercise:

gunzip

• gunzip gzip_file uncompress files (compress with gzip)
• gunzip -c gzip_file uncompress files, write output on standard output; keep original files unchanged.

exercise:

uncompress the files in Sequence/Proteique/

bzip2

• bzip2 is like gzip but with an other algorithm of compression.
• bunzip2 is like gunzip

create archive

GNU ‘tar’ saves many files together into a single tape or disk archive.

• as we work on file (not tape) all commands we use have file (-f) option

• -c to create an archive

• tar -cf archive.tar foo bar Create archive.tar from files foo and bar.

  tar -cf foo.tar Nucleique/3_seq.*
  

• usually we add .tar extension to the archive name.

create archive

• -C allow to change to directory DIR

exercise:

• go in Sequence directory and compare

  1. tar -cf archive Nucleique/3_seq.*
  2. tar -cf archive-C_option -C Nucleique 3_seq.*

create and compress an archive

• after creating an archive we can compress it with gzip

• but we can do this 2 operation with tar

• use option -z or -j for compress with gzip or bzip2 respectively.

  tar -czf  my_seq.tar.gz Nucleique/*
  tar -cjf  my_seq.tar.bz2 Nucleique/*
  

• usually we use double extension tar.gz or tar.bz2 .

• sometimes we use .tgz or .tbz

create and compress an archive

exercise:

• use gzip to compress archive and archive-C_option
• use the right options to do this in one operation (beware to the archive names).

list the content of an archive

To know what an archive contains use the -t option.

tar -tzf archive.tar.gz
tar -tjf archive.tar.bz2

tar -tzf toto.tar.gz
Nucleique/
Nucleique/qn1.gb
Nucleique/qr.fasta
Nucleique/collection_of_colstridium_genomesFASTA.txt
...

uncompress and restore an archive

To extract an archive use the -x option. To uncompress an archive use -z or -j option for gzip or bzip2 respectively.

tar -xzf archive.tar.gz
tar -xjf archive.tar.bz2

by default the extract is been wher the command is run we can change this using -C dir option.

tar -xjf archive.tar.bz2 -C Foobar

send an archive by mail

F*EX is the dl service at pasteur

• fexsend is the command

1. register fexsend -I

   fexsend -I
   F*EX server URL: http://dl.pasteur.fr/
   proxy address (hostname:port or empty if none):
   Your e-mail address as registered at http://dl.pasteur.fr/: nimort.naoik@pasteur.fr
   Your auth-ID for nimort.naoik@pasteur.fr at http://dl.pasteur.fr/: pick_an_id
   data written to /pasteur/homes/nnaoik/.fex/id
   

2. fexsend file recipient@domain.fr

send an archive by mail

exercise:

1. for those who have not a fex account go on http://dl.pasteur.fr/ and request an account
2. log on central-bio.pasteur.fr
3. send you one of the archive you did using F*EX

(documentaion: https://projets.pasteur.fr/projects/fex/wiki)